Molecular sequence of swine retrovirus and methods of use

ABSTRACT

Purified nucleic acid which can specifically hybridize with the sequence of swine retroviruses.

[0001] This application is a divisional of U.S. Ser. No. 09/661,858, filed on Sep. 14, 2000, which is a divisional of U.S. Ser. No. 08/766,528, filed on Dec. 13, 1996, which is a continuation-in-part of U.S. Ser. No. 08/572,645, filed on Dec. 14, 1995, the entire contents of which are hereby incorporated by reference.

FIELD OF THE INVENTION

[0002] The invention relates to porcine retroviral sequences, peptides encoded by porcine retroviral sequences, and methods of using the porcine retroviral nucleic acids and peptides.

BACKGROUND OF THE INVENTION

[0003] Advances in solid organ transplantation and a chronic shortage of suitable organ donors have made xenotransplantation an attractive alternative to the use of human allografts. However, the potential for introduction of a new group of infectious diseases from donor animals into the human population is a concern with the use of these methods.

[0004] The term applied to the natural acquisition by humans of infectious agents carried by other species is zoonosis. The transplantation of infection from nonhuman species into humans is best termed “direct zoonosis” or “xenosis.”

[0005] Nonhuman primates and swine have been considered the main potential sources of organs for xenotransplantation (Niekrasz et al. (1992) Transplant Proc 24:625; Starzl et al. (1993) Lancet 341:65; Murphy et al. (1970) Trans Proc 4:546; Brede and Murphy (1972) Primates Med 7:18; Cooper et al. In Xenotransplantation: The Transplantation of Organs and Tissues between Species, eds. Cooper et al. (1991) p. 457; R Y Calne (1970) Transplant Proc 2:550; H. Auchincloss, Jr. (1988) Transplantation 46:1; and Chiche et al. (1993) Transplantation 6:1418). The infectious disease issues for primates and swine are similar to those of human donors. The prevention of infection depends on the ability to predict, to recognize, and to prevent common infections in the immunocompromised transplantation recipient (Rubin et al. (1993) Antimicrob Agents Chemother 37:619). Because of the potential carriage by nonhuman primates of pathogens easily adopted to humans, ethical concerns, and the cost of maintaining large colonies of primates, other species have received consideration as organ donors (Brede and Murphy (1972) Primates Med 7:18; Van Der Riet et al. (1987) Transplant Proc 19:4069; Katler In Xenotransplantation: The Transplantation of Organs and Tissues between Species, eds. Cooper et al. (1991) p. 457; Metzger et al. (1981) J Immunol 127:769; McClure et al. (1987) Nature 330:487; Letvin et al. (1987) J Infect Dis 156:406; Castro et al. (1991) Virology 184:219; Benveniste and Todaro (1973) Proc Natl Acad Sci USA 70:3316; and Teich, in RNA Tumor viruses, eds. Weiss et. al. (1985) p. 25). The economic importance of swine and experience in studies of transplantation in the miniature swine model have allowed some of the potential pathogens associated with these animals to be defined (Niekrasz et al. (1992) Transplant Proc 24:625; Cooper et al. In Xenotransplantation: The Transplantation of Organs and Tissues between Species, eds. Cooper et al. (1991) p. 457; and Leman et al. (1992) Diseases of Swine, 7th ed. Ames, Iowa:Iowa State University). Miniature swine have received consideration as organ donors because of a number of features of the species. The structure and function of the main pig organs are comparable to those of man. Swine attain body weights and organ sizes adequate to the provision of organs for human use. Lastly, veterinarians and commercial breeders have developed approaches to creation of specific-pathogen-free (SPF) swine with the ability to eliminate known pathogens from breeding colonies (Alexander et al. (1980) Proc 6th Int Congr Pig Vet Soc, Copenhagen; Betts (1961) Vet Rec 73:1349; Betts et al. (1960) Vet Rec 72:461; Caldwell et al. (1959) J Am Vet Med Assoc 135:504; and Yong (1964) Adv Vet Sci 9:61).

[0006] Concern exists over the transfer of porcine retroviruses by xenotransplantation (Smith (1993) N Engl J Med 328:141). Many of the unique properties of the retroviruses are due to the synthesis of a complementary DNA copy from the RNA template (by reverse transcriptase), and integration of this DNA into the host genome. The integrated retroviral copy (which is referred to as an endogenous copy or “provirus”) can be transmitted via the germ line.

SUMMARY OF THE INVENTION

[0007] In general, the invention features a purified swine or miniature swine retroviral nucleic acid, e.g., a Tsukuba nucleic acid, a purified miniature swine retroviral nucleic acid sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, and methods of their use in detecting the presence of porcine, e.g., miniature swine, retroviral sequences.

[0008] In another aspect, the invention features a purified nucleic acid, e.g., a probe or primer, which can specifically hybridize with a purified swine or miniature swine retroviral genome, e.g., a Tsukuba genome, the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0009] In preferred embodiments the nucleic acid is other than the entire retroviral genome of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, e.g., it is at least 1 nucleotide longer, or at least 1 nucleotide shorter, or differs in sequence at at least one position, e.g., the nucleic acid is a fragment of the sequence of SEQ ID NO:1 or its complement SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, or it includes sequence additional to that of SEQ ID NO:1, or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0010] In preferred embodiments, the nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0011] In other embodiments: the sequence of the nucleic acid differs from the corresponding sequence of SEQ ID NO: 1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, by 1, 2, 3, 4, or 5 base pairs; the sequence of the nucleic acid differs from the corresponding sequence of SEQ ID NO: 1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, by at least 1, 2, 3, 4, or 5 base pairs but less than 6, 7, 8, 9, or 10 base pairs.

[0012] In other preferred embodiments: the nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length.

[0013] In yet other preferred embodiments: the nucleic acid can specifically hybridize with a translatable region of a miniature swine retroviral genome, e.g., the retroviral genome of SEQ ID NO: 1, or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, e.g., a region from the gag, pol, or env gene; the probe or primer can specifically hybridize with an untranslated region of a miniature swine retroviral genome, e.g., the retroviral genome of SEQ ID NO: 1, or its complement SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement; the probe or primer can specifically hybridize with a non-conserved region of a miniature swine retroviral genome, e.g., the retroviral genome of SEQ ID NO: 1, or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement; the probe or primer can specifically hybridize with the highly conserved regions of a miniature swine retroviral genome, e.g., the retroviral genome of SEQ ID NO: 1, or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0014] In preferred embodiments, the primer is selected from the group consisting of SEQ ID NOs:4-74.

[0015] In preferred embodiments, hybridization of the probe to retroviral sequences can be detected by standard methods, e.g., by radiolabeled probes or by probes bearing nonradioactive markers such as enzymes or antibody binding sites. For example, a probe can be conjugated with an enzyme such as horseradish peroxidase, where the enzymatic activity of the conjugated enzyme is used as a signal for hybridization. Alternatively, the probe can be coupled to an epitope recognized by an antibody, e.g., an antibody conjugated to an enzyme or another marker.

[0016] In another aspect, the invention features a reaction mixture which includes a target nucleic acid, e.g., a human, swine or a miniature swine nucleic acid, and a purified second nucleic acid, e.g., a probe or primer, as, e.g., is described herein, which specifically hybridizes with the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, a swine or a miniature swine retroviral nucleic acid, e.g., a Tsukuba nucleic acid. β

[0017] In preferred embodiments, the target nucleic acid: includes RNA; or includes DNA.

[0018] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a miniature swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ which has-been transplanted into a organ recipient, e.g., a xenogeneic recipient, e.g., a primate, e.g., a human.

[0019] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ which has been transplanted into a organ recipient, e.g., a xenogeneic recipient, e.g., a primate, e.g., a human.

[0020] In a preferred embodiment: the second nucleic acid is a porcine retroviral sequence, probe or primer, e.g., as described herein, e.g., a Tsukuba-1 retroviral sequence the second nucleic acid is a sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, or a fragment of the sequence or complement at least 10, 20, or 30, basepairs in length.

[0021] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0022] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0023] In preferred embodiments the second nucleic acid is: a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof.

[0024] In another aspect, the invention features a method for screening a cell or a tissue, e.g., a cellular or tissue transplant, e.g., a xenograft, for the presence or expression of a swine or a miniature swine retrovirus or retroviral sequence, e.g., an endogenous miniature swine retrovirus. The method includes:

[0025] contacting a target nucleic acid from the tissue with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid under conditions in which hybridization can occur, hybridization being indicative of the presence or expression of an endogenous miniature swine retrovirus or retroviral sequence in the tissue or an endogenous swine retrovirus in the tissue.

[0026] In preferred embodiments, the method further includes amplifying the target nucleic acid with primers which specifically hybridize to the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0027] In preferred embodiments, the tissue or cellular transplant is selected from the group consisting of: heart, lung, liver, bone marrow, kidney, brain cells, neural tissue, pancreas or pancreatic cells, thymus, or intestinal tissue.

[0028] In other preferred embodiments, the target nucleic acid is: DNA; RNA; or cDNA.

[0029] In other preferred embodiments, the target nucleic acid is taken from: a tissue sample, or a blood sample, e.g., a tissue biopsy sample, e.g., a tissue sample suitable for in situ hybridization or immunohistochemistry.

[0030] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a miniature swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ which has been transplanted into a organ recipient, e.g., a xenogeneic recipient, e.g., a primate, e.g., a human.

[0031] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ which has been transplanted into a organ recipient, e.g., a recipient swine or a xenogeneic recipient, e.g., a primate, e.g., a human.

[0032] In a preferred embodiment the target nucleic acid is RNA, or a nucleic acid amplified from RNA in the tissue, and hybridization is correlated with expression of an endogenous miniature swine retrovirus or retroviral sequence or an endogenous swine retrovirus.

[0033] In a preferred embodiment the target nucleic acid is DNA, or a nucleic acid amplified from DNA in the tissue, and hybridization is correlated with the presence of an endogenous miniature swine retrovirus or an endogenous swine retrovirus.

[0034] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0035] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0036] In another aspect, the invention features a method of screening a porcine derived cell or tissue for the presence of an activatable porcine retrovirus, e.g., an activatable porcine provirus. The method includes:

[0037] stimulating a porcine derived cell or tissue with a treatment which can activate a retrovirus;

[0038] contacting a target nucleic acid from the porcine derived cell or tissue with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid hybridization being indicative of the presence of an activatable porcine provirus in the porcine derived cell or tissue.

[0039] In preferred embodiments the treatment is: contact with a drug, e.g., a steroid or a cytotoxic agent, infection or contact with a virus, the induction of stress, e.g., nutritional stress or immunologic stress, e.g., contact with a T-cell, e.g., a reactive T-cell.

[0040] In preferred embodiments, the method further includes amplifying the target nucleic acid with primers which specifically hybridize to the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0041] In other preferred embodiments, the target nucleic acid is taken from: a tissue sample, or a blood sample, e.g., a tissue biopsy sample, e.g., a tissue sample suitable for in situ hybridization or immunohistochemistry.

[0042] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a miniature swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ which has been transplanted into a organ recipient, e.g., a xenogeneic recipient, e.g., a primate, e.g., a human.

[0043] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ which has been transplanted into a organ recipient, e.g., a recipient swine or a xenogeneic recipient, e.g., a primate, e.g., a human.

[0044] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0045] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0046] In another aspect, the invention features a method for screening a miniature swine genome or a swine genome for the presence of a porcine retrovirus or retroviral sequence, e.g., an endogenous porcine retrovirus. The method includes:

[0047] contacting the miniature swine (or swine) genomic DNA with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid under conditions in which the sequences can hybridize, hybridization being indicative of the presence of the endogenous porcine retrovirus or retroviral sequence in the miniature swine (or swine) genome.

[0048] In preferred embodiments, the method further includes amplifying all or a portion of the miniature swine (or swine) genome with primers which specifically hybridize to the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0049] In a preferred embodiment: the second nucleic acid is a porcine retroviral sequence, probe or primer, e.g., as described herein, e.g., a Tsukuba-1 retroviral sequence; the second nucleic acid is a sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, or a fragment of the sequence or complement at least 10, 20, or 30, basepairs in length.

[0050] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0051] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0052] In another aspect, the invention features a method for screening a genetically modified miniature swine or a genetically modified swine for the presence or expression of a miniature swine or swine retrovirus or retroviral sequence, e.g., an endogenous miniature swine retrovirus. The method includes:

[0053] contacting a target nucleic acid from the genetically modified miniature swine or swine with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid under conditions in which hybridization can occur, hybridization being indicative of the presence or expression of an endogenous miniature swine retrovirus or retroviral sequence or swine retrovirus or retroviral sequence in the genetically modified miniature swine or swine.

[0054] In preferred embodiments, the method further includes amplifying the target nucleic acid with primers which specifically hybridize to the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0055] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a miniature swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ which has been transplanted into a organ recipient, e.g., a xenogeneic recipient, e.g., a primate, e.g., a human.

[0056] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ which has been transplanted into a organ recipient, e.g., a recipient swine or a xenogeneic recipient, e.g., a primate, e.g., a human.

[0057] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0058] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0059] In another aspect, the invention features a method of assessing the potential risk associated with the transplantation of a graft from a donor miniature swine or swine into a recipient animal, e.g., a miniature swine or swine, a non-human primate, or a human. The method includes:

[0060] contacting a target nucleic acid from the donor, recipient or the graft, with a second sequence chosen from the group of: a nucleic acid sequence which specifically hybridizes a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof;

[0061] a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof;

[0062] a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid under conditions in which the sequences can hybridize, hybridization being indicative of a risk associated with the transplantation.

[0063] In a preferred embodiment: the second nucleic acid is a Tsukuba-1 retroviral sequence, probe or primer, e.g., as described herein; the second nucleic acid is a porcine retroviral sequence, probe or primer, e.g., as described herein; the second nucleic acid is the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, or a fragment of the sequence or complement at least 10, 20, or 30, basepairs in length.

[0064] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a miniature swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ which has been transplanted into a organ recipient, e.g., a xenogeneic recipient, e.g., a primate, e.g., a human.

[0065] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine potential donor organ; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ which has been transplanted into a organ recipient, e.g., a recipient swine or a xenogeneic recipient, e.g., a primate, e.g., a human.

[0066] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0067] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0068] In another aspect, the invention features a method of determining if an endogenous miniature swine or swine retrovirus or retroviral sequence genome includes a mutation which modulates its expression, e.g., results in misexpression. The method includes:

[0069] determining the structure of the endogenous retroviral genome, and

[0070] comparing the structure of the endogenous retroviral genome with the retroviral sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, a difference being predictive of a mutation.

[0071] In preferred embodiments the method includes sequencing the endogenous genome and comparing it with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0072] In preferred embodiments, the method includes using primers to amplify, e.g., by PCR, LCR (ligase chain reaction), or other amplification methods, a region of the endogenous retroviral genome, and comparing the structure of the amplification product to the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement to determine if there is difference in sequence between retroviral genome and SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement. The method further includes determining if one or more restriction sites exist in the endogenous retroviral genome, and determining if the sites exist in SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0073] In preferred embodiments, the mutation is a gross defect, e.g., an insertion, inversion, translocation or a deletion, of all or part of the retroviral genome.

[0074] In preferred embodiments, detecting the mutation can include: (i) providing a labeled PCR probe amplified from DNA (e.g., SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3) containing a porcine retroviral nucleotide sequence which hybridizes to a sense or antisense sequence from the porcine retroviral genome (e.g., SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3), or naturally occurring mutants thereof; (ii) exposing the probe/primer to nucleic acid of the tissue (e.g., genomic DNA) digested with a restriction endonuclease; and (iii) detecting by in situ hybridization of the probe/primer to the nucleic acid, the presence or absence of the genetic lesion. Alternatively, direct PCR analysis, using primers specific for porcine retroviral genes (e.g., genes comprising the nucleotide sequence shown in SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3), can be used to detect the presence or absence of the genetic lesion in the porcine retroviral genome by comparing the products amplified.

[0075] In another aspect, the invention features a method of providing a miniature swine or a swine free of an endogenous retrovirus or retroviral sequence, e.g., activatable retrovirus, insertion at a preselected site. The method includes:

[0076] performing a breeding cross between a first miniature swine (or swine) having a retroviral insertion at the preselected site and a second miniature swine (or swine) not having a retroviral insertion at a preselected site, e.g., the same site, and recovering a progeny miniature swine (or swine), not having the insertion, wherein the presence or absence of the retroviral insertion is determined by contacting the genome of a miniature swine (or swine) with a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof;

[0077] a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, of naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid.

[0078] In preferred embodiments, the nucleic acid is hybridized to nucleic acid, e.g., DNA from the genome, of the first animal or one of its ancestors.

[0079] In preferred embodiments, the nucleic acid is hybridized to nucleic acid, e.g., DNA from the genome, of the second animal or one of its ancestors.

[0080] In preferred embodiments, the nucleic acid is hybridized to nucleic acid, e.g., DNA from the genome, of the progeny animal or one of its descendants.

[0081] In preferred embodiments, the nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0082] In other preferred embodiments: the nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is a full length retroviral genome.

[0083] In another aspect, the invention features a method of evaluating a treatment, e.g., an immunosuppressive treatment, for the ability to activate a retrovirus, e.g., an endogenous porcine retrovirus. The method includes:

[0084] administering a treatment to a subject, e.g., a miniature swine (or a swine), having an endogenous porcine retrovirus; and

[0085] detecting expression of the porcine retrovirus with a purified nucleic acid sequence which specifically hybridizes to the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0086] In preferred embodiments, the immunosuppresive treatment includes radiation, chemotherapy or drug treatment.

[0087] In preferred embodiments: the treatment is one which can induce immunological tolerance; the treatment is one which can introduce new genetic material, e.g., introduce new genetic material into a miniature swine genome (or a swine genome) or into the genome of a host which receives a swine or a miniature swine graft, e.g., the treatment is one which introduces a new genetic material via retroviral mediated transfer.

[0088] In a preferred embodiment: the purified nucleic acid is a Tsukuba-1 retroviral sequence, probe or primer, e.g., as described herein; the purified nucleic acid is a porcine retroviral sequence, probe or primer, e.g., as described herein; the purified nucleic acid is the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, or a fragment of such sequence or complement at least 10, 20, or 30, basepairs in length.

[0089] In preferred embodiments, the purified nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0090] In other preferred embodiments: the purified nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100. 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the purified nucleic acid is a full length retroviral genome.

[0091] In preferred embodiments the second nucleic acid is: a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof.

[0092] In another aspect, the invention features a method of localizing the origin of a porcine retroviral infection. The method includes:

[0093] contacting a target nucleic acid from the graft with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof;

[0094] a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid contacting a target nucleic acid from the recipient with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid; hybridization to the nucleic acid from the graft correlates with the porcine retroviral infection in the graft; and hybridization to the nucleic acid from the recipient correlates with the porcine retroviral infection in the recipient.

[0095] In preferred embodiments, the target nucleic acid includes: genomic DNA, RNA or cDNA, e.g., cDNA made from an RNA template.

[0096] In a preferred embodiment: the second nucleic acid is a porcine retroviral sequence, probe or primer, e.g., as described herein, e.g., a Tsukuba-1 retroviral sequence; the second nucleic acid is a sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, or a fragment of the sequence or complement at least 10, 20, or 30, basepairs in length.

[0097] In preferred embodiments, the recipient is an animal, e.g., a miniature swine, a swine, a non-human primate, or a human.

[0098] In preferred embodiments, the graft is selected from the group consisting of: heart, lung, liver, bone marrow or kidney.

[0099] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0100] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0101] In another aspect, the invention features a method of screening a cell, e.g., a cell having a disorder, e.g., a proliferative disorder, e.g., a tumor cell, e.g., a cancer cell, e.g., a lymphoma or a hepatocellular carcinoma, developing in a graft recipient, e.g., a xenograft, for the presence or expression of a porcine retrovirus or retroviral sequence. The method includes:

[0102] contacting a target nucleic acid from a tumor cell with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid, under conditions in which the sample and the nucleic acid sequence can hybridize, hybridization being indicative of the presence of the endogenous porcine retrovirus or retroviral sequence in the tumor cell.

[0103] In preferred embodiments, the target nucleic acid from a tumor cell includes: genomic DNA, RNA or cDNA, e.g., cDNA made from an RNA template.

[0104] In a preferred embodiment: the second nucleic acid is a porcine retroviral sequence, probe or primer, e.g., as described herein, e.g., a Tsukuba-1 retroviral sequence; the second nucleic acid is a sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, or a fragment of the sequence or complement at least 10, 20, or 30, basepairs in length.

[0105] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0106] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0107] In another aspect, the invention features a method of screening a human subject for the presence or expression of an endogenous porcine retrovirus or retroviral sequence comprising:

[0108] contacting a target nucleic acid derived from the human subject with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or anti sense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid under conditions in which the sequences can hybridize, hybridization being indicative of the presence of the endogenous porcine retrovirus or retroviral sequence in the human subject.

[0109] In preferred embodiments, the target nucleic acid derived from a human subject is DNA, RNA or cDNA sample, nucleic acid from a blood sample or a tissue sample, e.g., a tissue biopsy sample.

[0110] In preferred embodiments, the human subject is a miniature swine or swine xenograft recipient, or a person who has come into contact with a miniature swine or swine xenograft recipient.

[0111] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0112] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0113] In preferred embodiments: the recipient is tested for the presence of porcine retroviral sequences prior to implantation of swine or miniature swine tissue.

[0114] In another aspect, the invention features a method of screening for viral mutations which modulate, e.g., increase or decrease, susceptibility of a porcine retrovirus to an antiviral agent, e.g., an antiviral antibiotic. The method includes:

[0115] administering a treatment, e.g., an antiviral agent, e.g., an antiviral antibiotic;

[0116] isolating a putative mutant porcine retroviral strain;

[0117] determining a structure of the putative mutant retroviral strain; and

[0118] comparing the structure to SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0119] In another aspect, the invention features a method of screening for viral mutations which modulate, e.g., increase or decrease, susceptibility of a porcine retrovirus to an antiviral agent, e.g., an antiviral antibiotic. The method includes:

[0120] growing the porcine retrovirus in a presence of a treatment, e.g., an antiviral agent, e.g., an antiviral antibiotic; and

[0121] determine the amount of porcine retroviral DNA synthesized by hybridizing the porcine retroviral DNA to a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid.

[0122] In preferred embodiments, the method further includes amplifying the porcine retroviral nucleic acid with primers which specifically hybridize to the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, e.g., by polymerase chain reaction quantitative DNA testing (PDQ).

[0123] In a preferred embodiment: the second nucleic acid is a Tsukuba-1 retroviral sequence, probe or primer, e.g., as described herein; the second nucleic acid is a porcine retroviral sequence, probe or primer, e.g., as described herein; the second nucleic acid is the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0124] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0125] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0126] In another aspect, the invention features a method for screening a porcine-derived product for the presence or expression of a swine or miniature swine retrovirus or retroviral sequence, e.g., an endogenous miniature swine retrovirus. The method includes:

[0127] contacting a target nucleic acid from the porcine-derived product with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid, under conditions in which hybridization can occur, hybridization being indicative of the presence or expression of an endogenous miniature swine or swine retrovirus or retroviral sequences in the porcine-derived product.

[0128] In preferred embodiments the product is: a protein product, e.g., insulin; a food product; or a cellular transplant, e.g., a swine or miniature swine cell which is to be transplanted into a host, e.g., a swine or miniature swine cell which is genetically engineered to express a desired product,

[0129] In preferred embodiments, the method further includes amplifying the target nucleic acid with primers which specifically hybridize to the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0130] In other preferred embodiments, the target nucleic acid is: DNA; RNA; or cDNA.

[0131] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0132] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0133] In another aspect, the invention features a transgenic miniature swine or swine having a transgenic element, e.g., a base change, e.g., a change from A to G, or an insertion or a deletion of one or more nucleotides at an endogenous porcine retroviral insertion site, e.g., a retroviral insertion which corresponds to the retroviral genome of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0134] In preferred embodiments, the transgenic element is a knockout, e.g., a deletion, insertion or a translocation, of one or more nucleic acids, which alters the activity of the endogenous porcine retrovirus.

[0135] In another aspect, the invention features a method of inhibiting expression of an endogenous porcine retrovirus, including: inserting a mutation, e.g. a deletion into the endogenous retrovirus.

[0136] In preferred embodiments, the endogenous porcine retrovirus is inactivated.

[0137] In preferred embodiments, the mutation can be a point mutation, an inversion, translocation or a deletion of one or more nucleotides of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0138] In another aspect, the invention features a method of detecting a recombinant virus or other pathogen, e.g., a protozoa or fungi. The method includes:

[0139] providing a pathogen having porcine retroviral sequence; and

[0140] determining if the pathogen includes non-porcine retroviral sequence, the presence of non-porcine retroviral sequence being indicative of viral recombination.

[0141] In preferred embodiments, the method further includes determining the structure of a retrovirus by comparing the retrovirus sequence with sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, a difference being indicative of viral recombination.

[0142] In preferred embodiments, the method further includes comparing the structure of the retrovirus with a human retroviral sequence, e.g., HTLV1, HIV1, or HIV2, a similarity in structure being indicative of viral recombination.

[0143] In another aspect, the invention features a method of determining the copy number, size, or completeness of a porcine retrovirus or retroviral sequence, e.g., in the genome of a donor, recipient or a graft. The method includes:

[0144] contacting a target nucleic acid from the donor, recipient or a graft, with a second sequence chosen from the group of: a sequence which can specifically hybridize to a porcine retroviral sequence; a sequence which can specifically hybridize to the sequence of SEQ ID NO:1 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2 or its complement; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3 or its complement; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a gag protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 (e.g, from nucleotides 3112-4683) of SEQ ID NO:1, nucleotides 598-2169 (e.g, from nucleotides 598-2169) of SEQ ID NO:2, or nucleotides 585-2156 (e.g, from nucleotides 585-2156) of SEQ ID NO:3, or naturally occurring mutants thereof;

[0145] a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a pol protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3, or naturally occurring mutants thereof;

[0146] a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence which encodes a env protein; a nucleic acid of at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 (e.g, from nucleotides 86-1999) of SEQ ID NO:1, nucleotides 4738-6722 (e.g, from nucleotides 4738-6722) of SEQ ID NO:2, or nucleotides 5620-7533 of SEQ ID NO:3, or naturally occurring mutants thereof; a swine or miniature swine retroviral nucleic acid; or a Tsukuba nucleic acid.

[0147] In preferred embodiments, the method further includes amplifying the porcine retroviral nucleic acid with primers which specifically hybridize to the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, e.g., by polymerase chain reaction quantitative DNA testing (PDQ) or nested PCR.

[0148] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a miniature swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a miniature swine organ which has been transplanted into a organ recipient, e.g., a xenogeneic recipient, e.g., a primate, e.g., a human.

[0149] In preferred embodiments, the target nucleic acid includes: genomic DNA isolated from a swine; RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine; DNA, RNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ, e.g., a kidney; RNA, DNA or cDNA, e.g., cDNA made from an RNA template, isolated from a swine organ which has been transplanted into a organ recipient, e.g., a xenogeneic recipient, e.g., a primate, e.g., a human.

[0150] In preferred embodiments, the second nucleic acid has at least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with a sequence from SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0151] In other preferred embodiments: the second nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the second nucleic acid is a full length retroviral genome.

[0152] In another aspect, the invention features a method for screening a tissue, e.g., a cellular or tissue transplant, e.g., a xenograft, or a tissue from a graft recipient, for the presence or expression of a swine or a miniature swine retroviral sequence, e.g., an endogenous miniature swine retrovirus. The method includes: contacting a tissue sample with an antibody specific for a retroviral protein, e.g., an anti-gag, pol, or env antibody, and thereby determining if the sequence is present or expressed.

[0153] In preferred embodiments the protein is encoded by a sequence from: the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0154] In preferred embodiments, the tissue is selected from the group consisting of: heart, lung, liver, bone marrow, kidney, brain cells, neural tissue, pancreas or pancreatic cells, thymus, or intestinal tissue.

[0155] A “purified preparation” or a “substantially pure preparation” of a polypeptide as used herein, means a polypeptide which is free from one or more other proteins, lipids, and nucleic acids with which it naturally occurs. Preferably, the polypeptide, is also separated from substances which are used to purify it, e.g., antibodies or gel matrix, such as polyacrylamide. Preferably, the polypeptide constitutes at least 10, 20, 50 70, 80 or 95% dry weight of the purified preparation. Preferably, the preparation contains: sufficient polypeptide to allow protein sequencing; at least 1, 10, or 100 μg of the polypeptide; at least 1, 10, or 100 mg of the polypeptide.

[0156] Specifically hybridize, as used herein, means that a nucleic acid hybridizes to a target sequence with substantially greater degree than it does to other sequences in a reaction mixture. By substantially greater means a difference sufficient to determine if the target sequence is present in the mixture.

[0157] A “treatment”, as used herein, includes any therapeutic treatment, e.g., the administration of a therapeutic agent or substance, e.g., a drug or irradiation.

[0158] A “purified preparation of nucleic acid”, is a nucleic acid which is one or both of: not immediately contiguous with one or both of the coding sequences with which it is immediately contiguous (i.e., one at the 5′ end and one at the 3′ end) in the naturally-occurring genome of the organism from which the nucleic acid is derived; or which is substantially free of a nucleic acid sequence or protein with which it occurs in the organism from which the nucleic acid is derived. The term includes, for example, a recombinant DNA which is incorporated into a vector, e.g., into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA or genomic DNA fragment produced by PCR or restriction endonuclease treatment) independent of other DNA sequences. Substantially pure DNA also includes a recombinant DNA which is part of a hybrid gene encoding additional sequences. A purified retroviral genome is a nucleic acid which is substantially free of host nucleic acid or viral protein.

[0159] “Homologous”, as used herein, refers to the sequence similarity between two polypeptide molecules or between two nucleic acid molecules. When a position in both of the two compared sequences is occupied by the same amino acid or base monomer subunit, e.g., if a position in each of two DNA molecules is occupied by adenine, then the molecules are homologous at that position. The percent of homology between two sequences is a function of the number of matching or homologous positions shared by the two sequences divided by the number of positions compared×100. For example, if 6 of 10, of the positions in two sequences are matched or homologous then the two sequences are 60% homologous. By way of example, the DNA sequences ATTGCC and TATGGC share 50% homology. Generally, a comparison is made when two sequences are aligned to give maximum homology. The term sequence identity has substantially the same meaning.

[0160] The term “provirus” or “endogenous retrovirus,” as used herein, refers to an integrated form of the retrovirus.

[0161] The terms “peptides”, “proteins”, and “polypeptides” are used interchangeably herein.

[0162] As used herein, the term “transgenic element” means a nucleic acid sequence, which is partly or entirely heterologous, i.e., foreign, to the animal or cell into which it is introduced but which is designed to be inserted, or is inserted, into the animal's genome in such a way as to alter the genome of the cell into which it is inserted. The term includes elements which cause a change in the sequence, or in the ability to be activated, of an endogenous retroviral sequence. Examples of transgenic elements include those which result in changes, e.g., substitutions (e.g., A for G), insertions or deletions of an endogenous retroviral sequence (or flanking regions) which result in inhibition of activation or misexpression of a retroviral product.

[0163] As used herein, the term “transgenic cell” refers to a cell containing a transgenic element.

[0164] As used herein, a “transgenic animal” is any animal in which one or more, and preferably essentially all, of the cells of the animal includes a transgenic element. The transgenic element can be introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection. This molecule may be integrated within a chromosome, or it may be extrachromosomally replicating DNA.

[0165] As described herein, one aspect of the invention features a pure (or recombinant) nucleic acid which includes a miniature swine (or swine) retroviral genome or fragment thereof, e.g., nucleotide sequence encoding a gag-pol or env polypeptide, and/or equivalents of such nucleic acids. The term “nucleic acid”, as used herein, can include fragments and equivalents. The term “equivalent” refers to nucleotide sequences encoding functionally equivalent polypeptides or functionally equivalent polypeptides which, for example, retain the ability to react with an antibody specific for a gag-pol or env polypeptide. Equivalent nucleotide sequences will include sequences that differ by one or more nucleotide substitutions, additions or deletions, such as allelic variants, and will, therefore, include sequences that differ from the nucleotide sequence of gag, pol, or env shown in herein due to the degeneracy of the genetic code.

[0166] “Misexpression”, as used herein, refers to a non-wild type pattern of gene expression, e.g., porcine retroviral, e.g., Tsukuba-1 gene expression, e.g., gag, pol or env gene expression. It includes: expression at non-wild type levels, i.e., over or under expression; a pattern of expression that differs from wild type in terms of the time or stage at which the gene is expressed, e.g., increased or decreased expression (as compared with wild type) at a predetermined developmental period or stage; a pattern of expression that differs from wild type in terms of decreased expression (as compared with wild type) in a predetermined cell type or tissue type; a pattern of expression that differs from wild type in terms of the splicing, size, amino acid sequence, post-translational modification, stability, or biological activity of the expressed, porcine retroviral, e.g., Tsukuba-1, polypeptides; a pattern of expression that differs from wild type in terms of the effect of an environmental stimulus or extracellular stimulus on expression of the porcine retroviral, e.g., Tsukuba-1 genes, e.g., a pattern of increased or decreased expression (as compared with wild type) in the presence of an increase or decrease in the strength of the stimulus.

[0167] Methods of the invention can be used with swine or miniature swine.

[0168] Endogenous retrovirus is a potential source of infection not always susceptible to conventional breeding practices. Many proviruses are defective and unable to replicate. Provirus, if intact, can be activated by certain stimuli and then initiate viral replication using the host's cellular mechanisms. Retroviral infection will often not harm the host cell. However, replication of virus may result in viremia, malignant transformation (e.g., via insertion of retroviral oncogenes), degeneration, or other insertional effects (e.g., gene inactivation). The effects of such infection may not emerge for many years. The spectrum of behavior of active lentiviral infection in humans is well described relative to HIV. These include AIDS, unusual infections and tumors, recombinant and other viruses, and antigenic variation which may prevent the generation of protective immunity by the infected host.

[0169] Screening of animals will allow elimination of donors with active replication of known viruses. Inactive proviruses can be detected with genetic probes and removed or inactivated. These novel approaches will allow the identification and elimination of potential human pathogens derived from swine in a manner not possible in the outbred human organ donor population and, thus, will be important to the development of human xenotransplantation.

[0170] The porcine retroviral sequences of the invention are also useful as diagnostic probes to detect activation of endogenous porcine retroviruses following transplantation and xenotransplantation of organs derived from swine or miniature swine. The porcine retroviral sequences of the invention also provide diagnostic tools necessary to assess the risks associated with transplantation of organs from swine or miniature swine into human recipients. These sequences are also useful for the longitudinal evaluation of retroviral activation in the human recipient of miniature swine-derived organs.

[0171] The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are described in the literature. See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols. 154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).

[0172] Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are described below. All publications mentioned herein are incorporated by reference. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

DETAILED DESCRIPTION OF THE DRAWINGS

[0173]FIG. 1 is the nucleotide sequence (SEQ ID NO: 1) of the Tsukuba-1 cDNA.

[0174]FIG. 2 is the nucleotide sequence (SEQ ID NO: 2) of a defective retroviral genome isolated from the retrovirus from the PK-15 cell line.

[0175]FIG. 3 is the nucleotide sequence (SEQ ID NO: 3) of a retrovirus found in miniature swine.

DETAILED DESCRIPTION

[0176] Miniature Swine Retroviruses

[0177] Transplantation may increase the likelihood of retroviral activation, if intact and infectious proviruses are present. Many phenomena associated with transplantation, e.g., immune suppression, graft rejection, graft-versus-host disease, viral co-infection, cytotoxic therapies, radiation therapy or drug treatment, can promote activation of retroviral expression.

[0178] Many species are thought to carry retroviral sequences in their genomic DNA. The number of intact (complete) retroviral elements that could be activated is often unknown. Once activated, swine-derived viruses would require the appropriate receptor on human tissues to spread beyond the transplanted organ. Most intact endogenous proviruses (usually types B and C), once activated, are not pathogenic. However, coinfection with other viruses, recombination with other endogenous viruses, or modification of viral behavior in the foreign human environment may alter the pathogenicity, organ specificity or replication of the retroviruses or other infectious agents.

[0179] The lack of sequence data on pig viruses has impeded efforts to assess the number of porcine sequences, or porcine retroviral sequences, that have incorporated into the human genome or the frequency of incorporation.

[0180] The inventor, by showing that the Tsukuba-1 retrovirus is found in miniature swine, and by providing the entire sequence of the porcine retroviral (Tsukuba-1) genome, has allowed assessment of the risk of endogenous retroviruses in general clinical practice and more importantly in xenotransplantation.

[0181] The porcine retroviral sequences of the invention can be used to determine the level (e.g., copy number) of intact (i.e., potentially replicating) porcine provirus sequences in a strain of xenograft transplantation donors. For example, the copy number of the miniature swine retroviral sequences can be determined by the Polymerase Chain Reaction DNA Quantitation (PDQ) method, described herein, or by other methods known to those skilled in the art. This quantitation technique will allow for the selection of animal donors, e.g., miniature swine donors, without an intact porcine retroviral sequence or with a lower copy number of viral elements.

[0182] The porcine retroviral sequences of the invention can be used to determine if mutations, e.g., inversions, translocations, insertions or deletions, have occurred in the endogenous porcine retroviral sequence. Mutated viral genomes may be expression-deficient. For example, genetic lesions can be identified by exposing a probe/primer derived from porcine retrovirus sequence to nucleic acid of the tissue (e.g., genomic DNA) digested with a restriction endonucleases or by in situ hybridization of the probe/primer derived from the porcine retroviral sequence to the nucleic acid derived from donor, e.g., miniature swine, tissue. Alternatively, direct PCR analysis, using primers specific for porcine retroviral genes (e.g., genes comprising the nucleotide sequence shown in SEQ ID NO: 1, 2, or 3), can be used to detect the presence or absence of the genetic lesion in the porcine retroviral genome.

[0183] Miniature swine retroviral sequences of the invention can also be use to detect viral recombinants within the genome, or in the circulation, cells, or transplanted tissue, between the porcine retrovirus and other endogenous human viruses or opportunistic pathogens (e.g. cytomegalovirus) of the immunocompromised transplant recipient. For example, pieces of the viral genome can be detected via PCR or via hybridization, e.g., Southern or Northern blot hybridization, using sequences derived from SEQ ID NO: 1, 2, or 3 as primers for amplification or probes for hybridization.

[0184] Miniature swine retroviral sequences of the invention, e.g., PCR primers, allow quantitation of activated virus. Sequences of the invention also allow histologic localization (e.g., by in situ hybridization) of activated retrovirus. Localization allows clinicians to determine whether a graft should be removed as a source of potential retroviral infection of the human host or whether the retroviral infection was localized outside the graft.

[0185] Sequences of the invention, e.g., PCR primers, allow the detection of actively replicating virus, e.g., by using reverse transcribed PCR techniques known in the art. Standard techniques for reverse transcriptase measurements are often complicated, species-specific, and are of low sensitivity and specificity, and false positive results may develop using full-length probes for Southern and Northern molecular blotting. Sequences of the invention allow for sensitive and specific assays for the activation of virus and this will allow performance of a wide variety of tests, some of which are outlined below.

[0186] The invention provides for the testing and development of donor animals having reduced numbers of intact proviral insertions. It also provides for the testing of immunosuppressive regimens less likely to provide the conditions for active replication of retrovirus. Conditions likely to activate one retrovirus are generally more likely to activate other viruses including unknown retroviruses and known human pathogens including cytomegalovirus, hepatitis B and C viruses, Human Immunodeficiency Viruses (I and II). Given the availability of preventative therapies for these infections, these therapies could be used prophylactically in patients known to be susceptible to the activation of porcine retrovirus.

[0187] The miniature swine retroviral sequences of the invention can be used to measure the response of the miniature swine retroviral infection in humans to therapy, e.g., immunomodulatory or antiviral therapy, e.g., antiviral agents, e.g., antiviral antibiotics. With HIV, susceptibility to antiviral antibiotics is determined by the genetic sequence of the reverse transcriptase gene (RT pol region) and other genes. The ability to determine the exact sequence of the retroviral genes will allow the detection of mutations occurring during infection which would then confer resistance of this virus to antiviral agents. Primers, e.g., for the RT-pol region, of the invention can be used to detect and to sequence clinical viral isolates from patients which have developed mutations by PDQ method described herein. The primers of the invention can also be used to determine whether tumor cells, e.g., cancer cells, e.g. lymphoma or hepatocellular carcinoma, developing in xenograft recipients contain porcine retroviral elements.

[0188] The porcine retroviral sequences of the invention can also be used to detect other homologous retroviruses and to determine whether these are the same or different as compared to the Tusukuba-1 retroviral sequences. For example, within a species, the polymerase genes are highly conserved. PCR assays aimed at the gag-pol region followed by sequence analysis allow for this detection of homologous viruses. The appropriate regions of the Tsukuba-1 virus can be determined by using sequences derived from SEQ ID NO:1, described herein, to identify additional 5′ and 3′ viral genomic sequences. As is discussed elsewhere herein, the sequences from SEQ ID NO: 1 were used to obtain the sequence of the PK-15 retroviral insert (SEQ ID NO:2) and of a retroviral insertion in a miniature swine (SEQ ID NO:3).

[0189] Miniature swine retroviral sequences of the invention can be used to screen donor animals and xenograft recipients after transplantation both for infection, and as a measure of the appropriate level of immune suppression, regarding susceptibility to infection. Physicians, medical staff, family, or individuals who come into contact with graft recipients, and others, can be screened for infection with virus derived from the xenograft recipient. Members of the population in general can also be screened. Such screening can be used for broad epidemiologic studies of the community. These methods can help in meeting the requirements of the F.D.A. regarding enhancing the safety of the recipients and of the community to exposure to new viruses introduced into the community by xenograft transplantation.

[0190] As is shown in Suzuka et al., 1986, FEBS 198:339, the swine retroviruses such as the Tsukuba-1 genome can exist as a circular molecule. Upon cloning the circular molecule is generally cleaved to yield a linear molecule. As will be understood by one skilled in the art, the start point and end point of the resulting linear molecule, and the relative subregions of the viral sequence will of course vary with the point of cleavage. For example, in the Suzuka et al. reference the LTR is shown to be in an internal fragment. This is indicated herein in that the order of gag, pol, env in SEQ ID NO 1 is shown as env, gag, pol, while elsewhere herein the order of these regions is given as the naturally occurring gag, pol, env order.

[0191] Primers Derived from the Porcine Retroviral (Tsukuba-1) Genome Sequence

[0192] A number of different primers useful in the methods of the invention have been described herein. One skilled in the art can identify additional primers from the viral sequence of SEQ ID NO:1 by using methods known in the art. For example, when trying to identify potentially useful primers one skilled in the art would look for sequences (sequences should be between about 15 and 30 nucleotides in length) which hybridize to SEQ ID NO:1 with high melting temperature; have a balanced distribution of nucleotides, e.g., a balanced distribution of A, T, C and Gs; have a terminal C or G; do not self-hybridize or internally complement.

[0193] Use of Primers Derived from the Porcine Retroviral (Tsukuba-1) Genome Sequence

[0194] I. Testing of Organs or Cells Prior to Transplantation

[0195] Potential donor animals can be screened for active retroviral replication prior to being used in transplantation. This allows avoidance of animals undergoing active viral replication. Replicating virus is often infectious in 100% of recipients, while nonreplicating, latent provirus generally causes infection in 5 to 25% of recipients.

[0196] II. Testing of Recipients

[0197] Serial samples, e.g., of white blood cells, can be obtained from a graft recipient monthly, e.g., for the first month and every three months thereafter. Tissue biopsies obtained for evaluation of graft function can be used to evaluate the activation of retroviral sequences or of the expression retroviral sequences in graft tissue. Samples can be screened for the presence of retrovirus infection both specifically for the homologous virus, for viral recombinants containing portions of the viral genome, and for other retroviruses, using, e.g., PCR primers for the pol region of the virus, which is the region most likely to be conserved. If virus is detected, quantitative PCR can be used to determine the relative stability of viral production. Cells isolated from xenograft recipients can be tested by cocultivation with permissive human and porcine (e.g., pig fallopian tube, pig macrophage, or pig testis) cell lines known to contain endogenous viruses. Isolated virus will be tested for homology with the parental strain and for mutations which might affect susceptibility to antiviral agents, e.g., antiviral antibiotics.

[0198] III. Testing of Surgical and Medical Personnel and Family Members of Graft Recipient

[0199] Samples, e.g., white blood cells, can be banked (archived) from the surgical and medical personnel and from family members of the recipient prior to transplantation and at three months intervals for the first year and at least annually thereafter. Epidemiologic studies can be performed on these samples as well. These samples can be tested if the recipient becomes viremic or if unusual clinical manifestations are noted in these individuals.

[0200] IV. Testing of Tumor Cells

[0201] Tumor cells which develop from a graft, or a graft recipient, can be tested for the presence of active retrovirus and for proviruses.

[0202] V. Testing of Patients

[0203] Patients can be retested for any significant change in clinical condition or for increased immune suppression of graft rejection which may be associated with an increased risk of viral activation.

[0204] Sequencing of the Porcine Retroviral (Tsukuba-1) Genome

[0205] A clone (Pλ8.8) containing the 8060 bp XhoI porcine retrovirus (Tsukuba-1) insert was used to transfect competent E. coli, and DNA was isolated for sequencing. The strategy used to sequence the 8060 bp porcine retrovirus genome included a combination of procedures which are outlined below.

[0206] Random fragments (1-3 kb) of the clone (Pλ8.8) were generated by sonication. The fragments were blunt-ended and were subcloned into the EcoRV site of the pBluescript SK vector. Plasmid DNA was prepared using a modified alkaline lysis procedure. DNA sequencing was performed using DyeDeoxy termination reactions (ABI). Base specific fluorescent dyes were used as labels. Sequencing reactions were analyzed on 4.75% polyacrylamide gels by an ABI 373A-S or 373S automated sequencer. Subsequent data analysis was performed on Sequencer™ 3.0 software. The following internal sequencing primers were synthesized: AP1 5′ GATGAACAGGCAGACATCTG 3′ (SEQ ID NO:48) AP2 5′ CGCTTACAGACAAGCTGTGA 3′ (SEQ ID NO:49) AP3 5′ AGAACAAAGGCTGGGAAAGC 3′ (SEQ ID NO:50) AP4 5′ ATAGGAGACAGCCTGAACTC 3′ (SEQ ID NO:51) AP5 5′ GGACCATTGTCTGACCCTAT 3′ (SEQ ID NO:52) AP6 5′ GTCAACACCTATACCAGCTC 3′ (SEQ ID NO:53) AP7 5′ CATCTGAGGTATAGCAGGTC 3′ (SEQ ID NO:54) AP8 5′ GCAGGTGTAGGAACAGGAAC 3′ (SEQ ID NO:55) AP9 5′ ACCTGTTGAACCATCCCTCA 3′ (SEQ ID NO:56) AP10 5′ CGAATGGAGAGATCCAGGTA 3′ (SEQ ID NO:57) AP11 5′ CCTGCATCACTTCTCTTACC 3′ (SEQ ID NO:58) AP12 5′ TTGCCTGCTTGTGGAATACG 3′ (SEQ ID NO:59) AP13 5′ CAAGAGAAGAAGTGGGGAATG 3′ (SEQ ID NO:60) AP14 5′ CACAGTCGTACACCACGCAG 3′ (SEQ ID NO:61) AP15 5′ GGGAGACAGAAGAAGAAAGG 3′ (SEQ ID.NO:62) AP16 5′ CGATAGTCATTAGTCCCAGG 3′ (SEQ ID NO:63) AP17 5′ TGCTGGTTTGCATCAAGACCG 3′ (SEQ ID NO:64) AP18 5′ GTCGCAAAGGCATACCTGCT 3′ (SEQ ID NO:65) AP19 5′ ACAGAGCCTCTGCTAAGAAG 3′ (SEQ ID NO:66) AP20 5′ GCAGCTGTTGACAATCATC 3′ (SEQ ID NO:67) AP21 5′ TATGAGGAGAGGGCTTGACT 3′ (SEQ ID NO:68) AP22 5′ AGCAGACGTGCTAGGAGGT 3′ (SEQ ID NO:69) AP23 5′ TCCTCTTGCTGTTTGCATC 3′ (SEQ ID NO:70) AP24 5′ CAGACACTCAGAACAGAGAC 3′ (SEQ ID NO:71) AP25 5′ ACATCGTCTAACCCACCTAG 3′ (SEQ ID NO:72) AP26 5′ CTCGTTTCTGGTCATACCTGA 3′ (SEQ ID NO:73) AP27 5′ GAGTACATCTCTCTAGGCA 3′ (SEQ ID NO:74) AP28 5′ TGCCTAGAGACATGTACTC 3′ (SEQ ID NO:4) AP29 5′ CCTCTTCTAGCCATTCCTTCA 3′ (SEQ ID NO:5)

[0207] The clone (Pλ8.8) containing the 8060 bp XhoI porcine retrovirus (Tsukuba-1) insert was deposited with ATCC on Dec. 27, 1995 (ATCC Deposit No.97396).

[0208] Determination of the Porcine Retroviral (Tsukuba-1) Copy Number in a Miniature Swine

[0209] Total genomic DNA was isolated from miniature swine kidney by the methods known in the art. The isolated genomic DNA was digested with either EcoRI or HindIII restriction enzyme. The DNA digests were electrophoresed on an agarose gel, Southern blotted and hybridized to the full-length, purified, Tsukuba-1 sequence (SEQ ID NO:1) under high stringency conditions (0.1×SSC, 65° C.). In both digested samples (EcoRI or HindIII) at least six copies of the high molecular fragments of the miniature swine genome (over 16 Kb in size) hybridized to SEQ ID NO:1, indicating the presence of homologous retroviral sequences in porcine DNA.

[0210] Susceptibility Testing by Polymerase Chain Reaction DNA Quantitation (PDQ)

[0211] Polymerase chain reaction (PCR) DNA quantitation (PDQ) susceptibility testing can be used to rapidly and directly measure nucleoside sensitivity of porcine retrovirus isolates. PCR can be used to quantitate the amount of porcine retroviral RNA synthesized after in vitro infection of peripheral blood mononuclear cells. The relative amounts of porcine retroviral RNA in cell lysates from cultures maintained at different drug concentrations reflect drug inhibition of virus replication. With the PDQ method both infectivity titration and susceptibility testing can be performed on supernatants from primary cultures of peripheral blood mononuclear cells.

[0212] The PDQ experiments can be performed essentially as described by Eron et al., PNAS USA 89:3241-3245, 1992. Briefly, aliquots (1501 μl) of serial dilutions of virus sample can be used to infect 2×10⁶ PHA-stimulated donor PBMCs in 1.5 ml of growth medium per well of a flat-bottom 24-well plate (Corning). Separate cell samples can be counted, harvested, and lysed at 48, 72 and 96 hr. Quantitative PCR and porcine retrovirus copy-number determination can then be performed in duplicate on each lysate.

[0213] The results of a PDQ infectivity titration assay can be used to determine the virus dilution and length of culture time employed in a subsequent PDQ susceptibility test. These parameters should be chosen so that the yield of porcine retrovirus specific PCR product for the untreated control infection would fall on the porcine retrovirus copy-number standard curve before the curve approached its asymptotic maximum, or plateau. PHA-stimulated donor PBMCs can be incubated with drug for 4 hr prior to infection. Duplicate wells in a 24-well plate should receive identical porcine retrovirus inocula for each drug concentration tested and for the untreated infected controls. Uninfected controls and drug toxicity controls should be included in each experiment. All cultures can be harvested and cells lysed for PCT after either 48 or 72 hr. Previously characterized isolates can be used as assay standards in each experiment.

[0214] Cell pellets can be lysed in various volumes of lysis buffer (50 mM KCl/10 mM Tris•HCl, pH 8.3/2.5 mM MgCl₂/0.5% Nonidet P-40/0.5% Tween 20/0.01% proteinase K) to yield a concentration of 1.2×10⁴ cell equivalents/μl. Uniformity to cell lysate DNA concentrations should be confirmed in representative experiments by enhancement of Hoechst 33258 fluorescence (Mini-Fluorometer, Hoefer).

[0215] A conserved primer pair can be synthesized according to the pol gene sequences. The primers can than be used to amplify a 1580-base pair fragment of the porcine retrovirus pol gene from 1.2×10⁵ cell equivalents of lysate by using PCR (GeneAmp, Cetus) under standard conditions. Amplifications should be repeated if porcine retrovirus DNA is amplifiable from reagent controls.

[0216] Porcine retrovirus pol gene amplification products can be specifically detected and quantitated as described (Conway, B. C. (1990) in Techniques in HIV Research, (Aldovani & Walker, eds.) (Stockton, N.Y.) pp.40-46). Heat-denatured PCR products can be hybridized in a Streptavidin-coated microtiter plate well with both biotinylated capture probe and horseradish peroxidase (HRP)-labeled detector probe [enzyme-linked oligonucleotide solution sandwich hybridization assay ((ELOSA), DuPont Medical Products, Billerica, Mass.) for 60 min at 37° C. After extensive washing to remove all reactants except probe-DNA hybrids, an HRP chromogen, tetramethylbenzidine (TMBlue, Transgenic Sciences, Worcester, Mass.), should be added to each well. The HRP-catalyzed color development should be stopped after 1 hr by addition of sulfuric acid to 0.65 M. Absorbance (OD) at 450 nm can be measured in an automated microtiter plate reader (SLT Labinstruments, Hillsborough, N.C.).

[0217] A standard curve of porcine retrovirus DNA copy number can be generated in each PCR by using a dilution series of cells containing one porcine proviral genome per cell.

[0218] Preparation of a Miniature Swine Having a Knockout of Tsukuba-1 Viral Sequence Using Isogenic DNA Targeting Vectors

[0219] Isogenic DNA, or DNA that is substantially identical in sequence between the targeting vector and the target DNA in the chromosomes, greatly increases the frequency for homologous recombination events and gene targeting efficiency. Using isogenic-DNA targeting vectors, targeting frequencies of 80% or higher can be achieved in mouse embryonic stem cells. This is in contrast to non-isogenic DNA vectors which normally yield targeting frequencies of around 0.5% to 5%, i.e., approximately two orders of magnitude lower than isogenic DNA vectors. Isogenic DNA constructs are predominantly integrated into chromosomes by homologous recombination rather than random integration. As a consequence, targeted mutagenesis of viral sequences, e.g., viral genes, can be carried out in biological systems including zygotes, which do not lend themselves to the use of elaborate selection protocols, resulting in production of animals, e.g., miniature swine, free of, or having a reduced number of, activatable viral sequences. In order for the isogenic DNA approach to be feasible, targeting vectors should be constructed from a source of DNA that is identical to the DNA of the organism to be targeted. Ideally, isogenic DNA targeting is carried out in inbred strains of animals, e.g., inbred miniature swine, in which all genetic loci are homozygous. Any animal of that strain can serve as a source for generating isogenic targeting vectors. This protocol for isogenic gene targeting is outlined in TeRiele et al., PNAS 89:5128-5132, 1992 and PCT/US92/07184, herein incorporated by reference. A protocol for producing Tsukuba-1 knockout miniature swine is described briefly below.

[0220] An insertion vector is designed as described by Hasty and Bradley (Gene Targeting Vectors for Mammalian Cells, in Gene Targeting: A Practical Approach, ed, Alexandra L. Joyner, IRL Press 1993). Insertion vectors require that only ore crossover event occur for integration by homologous recombination into the native locus. The double strand breaks, the two ends of the vector which are known to be highly recombinogenic, are located on adjacent sequences on the chromosome. The targeting frequencies of such constructions will be in the range of 30 to 50%. One disadvantage of insertion vectors, in general, concerns the sequence duplications that are introduced and that potentially make the locus unstable. All these constructions are made using standard cloning procedures.

[0221] Replacement vectors have also been extensively described by Hasty and Bradley. Conceptually more straight forward than the insertion vector, replacement vectors use an essentially co-linear fragment of a stretch of Tsukuba-1 genomic sequence. Preferably, the DNA sequence from which an isogenic replacement vector is constructed includes approximately 6 to 10 kb of uninterrupted DNA. Two crossovers, one on either side of the selectable marker causes the mutant targeting vector to become integrated and replace the wild-type gene.

[0222] Microinjection of the isogenic transgene DNA into one of the pronuclei of a porcine embryo at the zygote stage (one-cell embryo) is accomplished by modification of a protocol described earlier (Hammer et al. 1985, Nature 315, 680; Pursel et al. 1989, Science 244, 1281). The age and the weight of the donor pigs, e.g., haplotype specific mini-swine, are critical to success. Optimally, the animals are of age 8 to 10 months and weigh 70 to 85 lbs. This increases the probability of obtaining an adequate supply of one-cell embryos for microinjection of the transgenes. In order to allow for accurate timing of the embryo collections at this stage from a number of embryo donors, the gilts are synchronized using a preparation of synthetic progesterone (Regumate). Hormone implants are applied to designated gilts 30 days prior to the date of embryo collection. Twenty days later, ten days prior to the date of collection, the implants are removed and the animals are treated with additional hormones to induce superovulation to increase the number of embryos for microinjection. Three days following implant removal, the animals are treated with 400 to 1000 IU of pregnant mare serum gonadotropin (PMSG) and with 750 IU of human chorionic gonadotropin (hCG) three to four days later. These animals are bred by artificial insemination (AI) on two consecutive days following injection of hCG.

[0223] Embryo collections are performed as follows: three days following the initial injection of hCG, the animals are anesthetized with an intramuscular injection of Telazol (3 mg/lb), Rompum (2 mg/lb) and Atropine (1 mg/lb). A midline laparotomy is performed and the reproductive tract exteriorized. Collection of the zygotes is performed by cannulating the ampulla of the oviduct and flushing the oviduct with 10 to 15 ml phosphate buffered saline, prewarmed to 39° C. Following the collection the donor animals are prepared for recovery from surgery according to USDA guidelines. Animals used twice for embryo collections are euthanized according to USDA guidelines.

[0224] Injection of the transgene DNA into the pronuclei of the zygotes is carried out as summarized below: Zygotes are maintained in medium HAM F-12 supplemented with 10% fetal calf serum at 38° C. in 5% CO₂ atmosphere. For injection the zygotes are placed into BMOC-2 medium, centrifuged at 13,000 g to partition the embryonic lipids and visualize the pronuclei. The embryos are placed in an injection chamber (depression slide) containing the same medium overlaid with light paraffin oil. Microinjection is performed on a Nikon Diaphot inverted-microscope equipped with Nomarski optics and Narishige micromanipulators. Using 40× lens power the embryos are held in place with a holding pipette and injected with a glass needle which is back-filled with the solution of DNA containing the transgenic element, e.g., a mutant viral gene (2 μg/ml). Injection of approximately 2 picoliters of the solution (4 femptograms of DNA), which is equivalent to around 500 copies of the transgenic element, e.g., a mutant viral gene, is monitored by the swelling of the pronucleus by about 50%. Embryos that are injected are placed into the incubator prior to transfer to recipient animals.

[0225] Recipient animals are prepared similarly to the donor animals, but not superovulated. Prior to the transfer of the injected embryos, recipient gilts are anesthetized, the abdomen opened surgically by applying a longitudinal incision and the ovaries exteriorized. The oviduct ipsilateral to the ovary with the larger number of corpus lutei is flushed, the embryos checked to evaluate if the animals is reproductively sound. Approximately 4 to 6 zygotes injected with the transgenic element, e.g., a mutant viral gene, are transferred to the flushed oviduct, the abdominal incision sutured and the animals placed in a warm area for recovery. The status of the pregnancy is monitored by ultrasound starting at day 25, or approximately one week following the expected date of implantation. Pregnant recipients are housed separately until they are due to farrow.

[0226] Newborn piglets are analyzed for integration of the transgenic element into chromosomal DNA. Genomic DNA is extracted from an ear punch or a blood sample and initial screening is performed using PCR. Animals that are potentially transgenic element-positive are confirmed by Southern analysis. Transgenic founder animals are subjected to further analysis regarding the locus of transgenic element integration using Southern analysis.

[0227] The Isolation and Sequencing of an Endogenous Swine Retroviral Insert and of a Retroviral Insert in Porcine PK-15 Cells

[0228] Cloning of PK15 and PAL Endogenous Retroviruses

[0229] I. Poly A⁺ RNA Isolation

[0230] Peripheral blood lymphocytes (PBLs) were prepared from haplotype d/d miniswine using standard protocols known in the art. The PBLs were cultured in the presence of 1% phytohemagglutinin (PHA) for about 84 hours. The activated PBLs were collected and total RNA was isolated using commercially available kits, such at Gentra's (Minneapolis, Minn.) PUREscript Kit. Poly A+RNA was isolated from the total RNA using another commercially available product, Dynal Dynabeads (Lake Success, N.Y.). Northern analysis of the RNA using a pig retroviral probe confirmed the presence of potentially full-length retroviral genome RNA. RNA from PK15 cells was isolated using similar protocols.

[0231] II. Construction of the cDNA Libraries

[0232] Using Superscript Choice System (Life Technologies Ltd, Gibco BRL, Gaithersburg, Md.) for cDNA Synthesis, a cDNA library was constructed using oligo dT to make the first strand cDNA. The use of Superscript reverse transcriptase was important in order to obtain full-length retroviral (RV) cDNAs, due to the length of the RV RNA. The cDNA library was enriched for large cDNA fragments by size selecting >4 kb fragments by gel electrophoresis. The cDNAs were cloned into Lambda ZAP Express (Clontech Laboratories, Inc. Palo Alto, Calif.), which is one of the few commercially available cDNA vectors that would accept inserts in the 1-12 kb range.

[0233] III. Screening of the cDNA Libraries

[0234] 0.75-1.2×10⁶ independent clones were screened using either gag and pol or gag and env probes. Double positive clones were further purified until single isolates were obtained (1 or 2 additional rounds of screening).

[0235] IV. Characterization of the Clones

[0236] Between 18 and 30 double positive clones were selected for evaluation. Lambda DNA was prepared using standard protocols, such as the Lambda DNA Kit (Qiagen Inc., Chatsworth, Calif.). The clones were analyzed by PCR to check for (a) RV genes, and (b) determine the size of insert and LTR regions. Restriction digests were also done to confirm the size of insert and to attempt to categorize the clones. Clones containing the longest inserts and having consistent and predicted PCR data were sequenced.

[0237] Development of a PCR-Based Assay for the Detection of the Presence of an Endogenous Retrovirus in Cells, Tissues, Organs, Miniswine or Recipient Hosts (e.g. Primates, Humans)

[0238] Using a commercially available computer software program (such as RightPrimer, Oligo 4.0, MacVector or Geneworks), one can analyze sequences disclosed herein for the selection of PCR primer pairs. The criteria for the general selection of primer pairs includes:

[0239] a. The Tm of each primer is between 65-70° C.

[0240] b. The Tm's for each pair differ by no more than 3° C.

[0241] c. The PCR fragment is between 200-800 bp in length

[0242] d. There are no repeats, self complementary bases, primer-dimer issues, etc for each pair

[0243] A. Additional Criteria for: A Pig-Specific PCR Assay

[0244] a. Primers are selected within porcine-specific regions of the sequence—such as within gag, env, or U3. Porcine-specific primers are defined as sequences which overall have <70% homology to the corresponding region in human, mouse and primate retroviruses. In addition, the last five bases at the 3′ end of the primer should be unique to the pig retroviral sequence.

[0245] b. Primers should have no more than one or two mismatched bases based on the miniswine, and retroviral sequences disclosed herein. These mismatched bases should not be within the last three or four bases of the 3′ end of the primer.

[0246] B. Additional Criteria for: Miniswine-Specific PCR Assay

[0247] a. Primers are selected such that there are at least one or two mismatches between miniswine and domestic pig sequences. At least one of these mismatches should be located within the last three or four bases at the 3′ end of the primer. Preferably, these mismatches would be a change from either a G or C in miniswine to either an A or T in domestic pig.

[0248] RT-PCR Strategy

[0249] There are a number of commercially available RT-PCR Kits for routine amplification of fragments. Several primer pairs should be tested to confirm Tm and specificity. Location of primers within the sequence depends in part on what question is being answered. RT-PCR should answer questions about expression and presence of RV sequences. PCR will not necessarily answer the question of whether the retroviral sequence is full-length or encodes a replication competent retrovirus. A positive signal in these tests only says there is RV sequence present. Indication of the possibility of full-length viral genomes being present can be obtained by performing long PCR using primers in U5 and U3. A commercial kit for long RT-PCR amplification is available (Takara RNA LA PCR Kit). Confirmation of full-length viral genomes requires infectivity studies and/or isolation of viral particles.

[0250] Northern analyses would complement RT-PCR data. Detection of bands at the predicted size of full-length viral genomes with hybridization probes from env, U3 or U5 would provide stronger evidence. The presence of other small bands hybridizing would indicate the amount of defective viral fragments present.

[0251] ELISA-Based Assay to Detect the Presence of Porcine Retroviral Proteins, Polypeptides or Peptides

[0252] In addition to the use of nucleic acid-based, e.g., PCR-based assays, to detect the presence of retroviral sequences, ELISA based assays can detect the presence of porcine retroviral proteins, polypeptides and peptides.

[0253] The basic steps to developing an ELISA include (a) generation of porcine retroviral specific peptides, polypeptides and proteins; (b) generation of antibodies which are specific for the porcine retroviral sequences; (c) developing the assay.

[0254] Using the retroviral sequences disclosed herein, antigenic peptides can be designed using computer based programs such as MacVector or Geneworks to analyse the retroviral sequences. Alternatively, it is possible to express the porcine retroviral sequences in gene expression systems and to purify the expressed polypeptides or proteins. After synthesis, the peptides, polypeptides or proteins are used to immunize mice or rabbits and to develop serum containing antibodies.

[0255] Having obtained the porcine retroviral specific antibodies the ELISA can be developed as follows. ELISA plates are coated with a volume of polyclonal or monoclonal antibody (capture antibody) which is reactive with the analyte to be tested. Such analytes include porcine retroviruses or retroviral proteins such as env or p24. The ELISA plates are then incubated at 4° C. overnight. The coated plates are then washed and blocked with a volume of a blocking reagent to reduce or prevent non-specific hybridization. Such blocking reagents include bovine serum albumin (BSA), fetal bovine serum (FBS), milk, or gelatin. The temperature for the blocking process is 37° C. Plates can be used immediately or stored frozen at −20° C. until needed. The plates are then washed, loaded with a serial dilution of the analyte, incubated at 37° C., and washed again. Bound analyte is detected using a detecting antibody. Detecting antibodies include enzyme-linked, fluoresceinated, biotin-conjugated or other tagged polyclonal or monoclonal antibodies which are reactive with the analyte. If monoclonal antibodies are used the detecting antibody should recognize an epitope which is different from the capture antibody.

Other Embodiments

[0256] In another aspect, the invention provides a substantially pure nucleic acid having, or comprising, a nucleotide sequence which encodes a swine or miniature swine, e.g., a Tsukuba-1 retroviral gag polypeptide.

[0257] In preferred embodiments: the nucleic acid is or includes the nucleotide sequence from nucleotides 2452-4839 of SEQ ID NO:1; the nucleic acid is at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homologous with a nucleic acid sequence corresponding to nucleotides 2452-4839 of SEQ ID NO:1; or by a sequence which, hybridizes under high stringency conditions to nucleotides 2452-4839 of SEQ ID NO:1; the nucleic acid includes a fragment of SEQ ID NO:1 which is at least 25, 50, 100, 200, 300, 400, 500, or 1,000 bases in length; the nucleic acid differs from the nucleotide sequence corresponding to nucleotides 2452-4839 of SEQ ID NO:1 due to degeneracy in the genetic code; the nucleic acid differs from the nucleic acid sequence corresponding to nucleotides 2452-4839 of SEQ ID NO:1 by at least one nucleotide but by less than 5, 10, 15 or 20 nucleotides and preferably which encodes an active peptide.

[0258] In yet another preferred embodiment, the nucleic acid of the invention hybridizes under stringent conditions to a nucleic acid probe corresponding to at least 12 consecutive nucleotides from nucleotides 2452-4839 of SEQ ID NO:1, or more preferably to at least 20 consecutive nucleotides from nucleotides 2452-4839 of SEQ ID NO:1, or more preferably to at least 40 consecutive nucleotides from nucleotides 2452-4839 of SEQ ID NO:1.

[0259] In another aspect, the invention features, a purified recombinant nucleic acid having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a nucleotide sequence corresponding to nucleotides 2452-4839 of SEQ ID NO:1.

[0260] The invention also provides a probe or primer which includes or comprises a substantially purified oligonucleotide. The oligonucleotide includes a region of nucleotide sequence which hybridizes under stringent conditions to at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2452-4839 of SEQ ID NO:1, or naturally occurring mutants thereof. In preferred embodiments, the probe or primer further includes a label attached thereto. The label can be, e.g., a radioisotope, a fluorescent compound, an enzyme, and/or an enzyme co-factor. Preferably the oligonucleotide is at least 10 and less than 20, 30, 50, 100, or 150 nucleotides in length. Preferred primers of the invention include oligonucleotides having a nucleotide sequence shown in any of SEQ ID NOs:32-37.

[0261] The invention involves nucleic acids, e.g., RNA or DNA, encoding a polypeptide of the invention. This includes double stranded nucleic acids as well as coding and antisense single strands.

[0262] In another aspect, the invention provides a substantially pure nucleic acid having, or comprising, a nucleotide sequence which encodes a swine or miniature swine, e.g., a Tsukuba-1 retroviral pol polypeptide.

[0263] In preferred embodiments: the nucleic acid is or includes the nucleotide sequence corresponding to nucleotides 4871-8060 of SEQ ID NO:1; the nucleic acid is at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homologous with a nucleic acid sequence corresponding to nucleotides 4871-8060 of SEQ ID NO:1; or by a sequence which, hybridizes under high stringency conditions to nucleotides 4871-8060 of SEQ ID NO:1; the nucleic acid includes a fragment of SEQ ID NO:1 which is at least 25, 50, 100, 200, 300, 400, 500, or 1,000 bases in length; the nucleic acid differs from the nucleotide sequence corresponding to nucleotides 4871-8060 of SEQ ID NO:1 due to degeneracy in the genetic code; the nucleic acid differs from the nucleic acid sequence corresponding to nucleotides 4871-8060 of SEQ ID NO:1 by at least one nucleotide but by less than 5, 10, 15 or 20 nucleotides and preferably which encodes an active peptide.

[0264] In yet another preferred embodiment, the nucleic acid of the invention hybridizes under stringent conditions to a nucleic acid probe corresponding to at least 12 consecutive nucleotides from nucleotides 4871-8060 of SEQ ID NO:1, or more preferably to at least 20 consecutive nucleotides from nucleotides 4871-8060 of SEQ ID NO:1, or more preferably to at least 40 consecutive nucleotides from nucleotides 4871-8060 of SEQ ID NO:1.

[0265] In another aspect, the invention features, a purified recombinant nucleic acid having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a nucleotide sequence corresponding to nucleotides 4871-8060 of SEQ ID NO:1.

[0266] The invention also provides a probe or primer which includes or comprises a substantially purified oligonucleotide. The oligonucleotide includes a region of nucleotide sequence which hybridizes under stringent conditions to at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 4871-8060 of SEQ ID NO:1, or naturally occurring mutants thereof. In preferred embodiments, the probe or primer further includes a label attached thereto. The label can be, e.g., a radioisotope, a fluorescent compound, an enzyme, and/or an enzyme co-factor. Preferably the oligonucleotide is at least 10 and less than 20, 30, 50, 100, or 150 nucleotides in length. Preferred primers of the invention include oligonucleotides having a nucleotide sequence shown in any of SEQ ID NOs:38-47.

[0267] The invention involves nucleic acids, e.g., RNA or DNA, encoding a polypeptide of the invention. This includes double stranded nucleic acids as well as coding and antisense single strands.

[0268] In another aspect, the invention provides a substantially pure nucleic acid having, or comprising, a nucleotide sequence which encodes a swine or miniature swine, e.g., a Tsukuba-1 retroviral env polypeptide.

[0269] In preferred embodiments: the nucleic acid is or includes the nucleotide sequence corresponding to nucleotides 2-1999 of SEQ ID NO:1; the nucleic acid is at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homologous with a nucleic acid sequence corresponding to nucleotides 2-1999 of SEQ ID NO:1; or by a sequence which, hybridizes under high stringency conditions to nucleotides 2-1999 of SEQ ID NO:1; the nucleic acid includes a fragment of SEQ ID NO:1 which is at least 25, 50, 100, 200, 300, 400, 500, or 1,000 bases in length; the nucleic acid differs from the nucleotide sequence corresponding to nucleotides 2-1999 of SEQ ID NO:1 due to degeneracy in the genetic code; the nucleic acid differs from the nucleic acid sequence corresponding to nucleotides 2-1999 of SEQ ID NO:1 by at least one nucleotide but by less than 5, 10, 15 or 20 nucleotides and preferably which encodes an active peptide.

[0270] In yet another preferred embodiment, the nucleic acid of the invention hybridizes under stringent conditions to a nucleic acid probe corresponding to at least 12 consecutive nucleotides from nucleotides 2-1999 of SEQ ID NO:1, or more preferably to at least 20 consecutive nucleotides from nucleotides 2-1999 of SEQ ID NO:1, or more preferably to at least 40 consecutive nucleotides from nucleotides 2-1999 of SEQ ID NO:1.

[0271] In another aspect, the invention features, a purified recombinant nucleic acid having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a nucleotide sequence corresponding to nucleotides 2-1999 of SEQ ID NO:1.

[0272] The invention also provides a probe or primer which includes or comprises a substantially purified oligonucleotide. The oligonucleotide includes a region of nucleotide sequence which hybridizes under stringent conditions to at least 10 consecutive nucleotides of sense or antisense sequence from nucleotides 2-1999 of SEQ ID NO:1, or naturally occurring mutants thereof. In preferred embodiments, the probe or primer further includes a label attached thereto. The label can be, e.g., a radioisotope, a fluorescent compound, an enzyme, and/or an enzyme co-factor. Preferably the oligonucleotide is at least 10 and less than 20, 30, 50, 100, or 150 nucleotides in length. Preferred primers of the invention include oligonucleotides having a nucleotide sequence shown in any of SEQ ID NOs:6-31.

[0273] The invention includes nucleic acids, e.g., RNA or DNA, encoding a polypeptide of the invention. This includes double stranded nucleic acids as well as coding and antisense single strands.

[0274] Included in the invention are: allelic variations, natural mutants, induced mutants, that hybridize under high or low stringency conditions to the nucleic acid of SEQ ID NO:1, 2, or 3 (for definitions of high and low stringency see Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1989, 6.3.1-6.3.6, hereby incorporated by reference).

[0275] The invention also includes purified preparations of swine or miniature swine retroviral polypeptides, e.g., gag pol, or env polypeptides, or fragments thereof, preferably biologically active fragments, or analogs, of such polypeptides. In preferred embodiments: the polypeptides are miniature swine retroviruses polypeptides; the polypeptides are Tsukuba polypeptides; the polypeptides are gag, pol, or env polypeptides encoded by SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, or naturally occuring variants thereof.

[0276] A biologically active fragment or analog is one having any in vivo or in vitro activity which is characteristic of the Tsukuba-1 polypeptides described herein, or of other naturally occurring Tsukuba-1 polypeptides. Fragments include those expressed in native or endogenous cells, e.g., as a result of post-translational processing, e.g., as the result of the removal of an amino-terminal signal sequence, as well as those made in expression systems, e.g., in CHO cells. A useful polypeptide fragment or polypeptide analog is one which exhibits a biological activity in any biological assay for Tusukuba-1 polypeptide activity. Most preferably the fragment or analog possesses 10%, preferably 40%, or at least 90% of the activity of Tsukuba-1 polypeptides, in any in vivo or in vitro Tsukuba-1 polypeptide assay.

[0277] In order to obtain a such polypeptides, polypeptide-encoding DNA can be introduced into an expression vector, the vector introduced into a cell suitable for expression of the desired protein, and the peptide recovered and purified, by prior art methods. Antibodies to the polypeptides can be made by immunizing an animal, e.g., a rabbit or mouse, and recovering antibodies by prior art methods.

[0278] The invention also features a purified nucleic acid, which has least 60%, 70%, 72%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, most preferably at least 98%, 99% or 100% sequence identity or homology with SEQ ID NO:1 or its complement, SEQ ID NO: 2 or its complement, or SEQ ID NO: 3 or its complement.

[0279] In preferred embodiments the nucleic acid is other than the entire retroviral genome of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, e.g., it is at least 1 nucleotide longer, or at least 1 nucleotide shorter, or differs in sequence at at least one position. E.g., the nucleic acid is a fragment of the sequence of SEQ ID NO:1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, or it includes sequence additional to that of SEQ ID NO:1, or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement.

[0280] In preferred embodiments: the sequence of the nucleic acid differs from the corresponding sequence of SEQ ID NO: 1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, by 1, 2, 3, 4, or 5 base pairs; the sequence of the nucleic acid differs from the corresponding sequence of SEQ ID NO: 1 or its complement, SEQ ID NO:2 or its complement, or SEQ ID NO:3 or its complement, by at least 1, 2, 3, 4, or 5 base pairs but less than 6, 7, 8, 9, or 10 base pairs.

[0281] In other preferred embodiments: the nucleic acid is at least 10, more preferably at least 15, more preferably at least 20, most preferably at least 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length; the nucleic acid is less than 15, more preferably less than 20, most preferably less than 25, 30, 50, 100, 1000, 2000, 4000, 6000, or 8060 nucleotides in length.

[0282] Equivalents

[0283] Those skilled in the art will be able to recognize, or be able to ascertain using no more than routine experimentation, numerous equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the following claims.

1 74 8060 base pairs nucleic acid single linear cDNA 1 CTCGAGACTC GGTGGAAGGG CCCTTATCTC GTACTTTTGA CCACACCAAC GGCTGTGAAA 60 GTCGAAGGAA TCTCCACCTG GATCCATGCA TCCCACGTTA AGCCGGCGCC ACCTCCCGAT 120 TCGGGGTGGA AAGCCGAAAA GACTGAAAAT CCCCTTAAGC TTCGCCTCCA TCGCGTGGTT 180 CCTTACTCTG TCAATAACCT CTCAGACTAA TGGTATGCGC ATAGGAGACA GCCTGAACTC 240 CCATAAACCC TTATCTCTCA CCTGGTTAAT TACTGACTCC GGCACAGGTA TTAATATCAA 300 CAACACTCAA GGGGAGGCTC CTTTAGGAAC CTGGTGGCCT GATCTATACG TTTGCCTCAG 360 ATCAGTTATT CCTAGTCTGA CCTCACCCCC AGATATCCTC CATGCTCACG GATTTTATGT 420 TTGCCCAGGA CCACCAAATA ATGGAAAACA TTGCGGAAAT CCCAGAGATT TCTTTTGTAA 480 ACAATGGAAC TGTGTAACCT CTAATGATGG ATATTGGAAA TGGCCAACCT CTCAGCAGGA 540 TAGGGTAAGT TTTTCTTATG TCAACACCTA TACCAGCTCT GGACAATTTA ATTACCTGAC 600 CTGGATTAGA ACTGGAAGCC CCAAGTGCTC TCCTTCAGAC CTAGATTACC TAAAAATAAG 660 TTTCACTGAG AAAGGAAAAC AAGAAAATAT CCTAAAATGG GTAAATGGTA TGTCTTGGGG 720 AATGGTATAT TATGGAGGCT CGGGTAAACA ACCAGGCTCC ATTCTAACTA TTCGCCTCAA 780 AATAAACCAG CTGGAGCCTC CAATGGCTAT AGGACCAAAT ACGGTCTTGA CGGGTCAAAG 840 ACCCCCAACC CAAGGACCAG GACCATCCTC TAACATAACT TCTGGATCAG ACCCCACTGA 900 GTCTAGCAGC ACGACTAAAA TGGGGGCAAA ACTTTTTAGC CTCATCCAGG GAGCTTTTCA 960 AGCTCTTAAC TCCACGACTC CAGAGGCTAC CTCTTCTTGT TGGCTATGCT TAGCTTTGGG 1020 CCCACCTTAC TATGAAGGAA TGGCTAGAAG AGGGAAATTC AATGTGACAA AAGAACATAG 1080 AGACCAATGC ACATGGGGAT CCCAAAATAA GCTTACCCTT ACTGAGGTTT CTGGAAAAGG 1140 CACCTGCATA GGAAAGGTTC CCCCATCCCA CCAACACCTT TGTAACCACA CTGAAGCCTT 1200 TAATCAAACC TCTGAAAGTC AATATCTGGT ACCTGGTTAT GACAGGTGGT GGGCATGTAA 1260 TACTGGATTA ACCCCTTGTG TTTCCACCTT GGTTTTTAAC CAAACTAAAG ATTTTTGCAT 1320 TATGGTCCAA ATTGTTCCCC GAGTGTATTA CTATCCCGAA AAAGCAATCC TTGATGAATA 1380 TGACTACAGA AATCATCGAC AAAAGAGAGA ACCCATATCT CTGACACTTG CTGTGATGCT 1440 CGGACTTGGA GTGGCAGCAG GTGTAGGAAC AGGAACAGCT GCCCTGGTCA CGGGACCACA 1500 GCAGCTAGAA ACAGGACTTA GTAACCTACA TCGAATTGTA ACAGAAGATC TCCAAGCCCT 1560 AGAAAAATCT GTCAGTAACC TGGAGGAATC CCTAACCTCC TTATCTGAAG TAGTCCTACA 1620 GAATAGAAGA GGGTTAGATT TATTATTTCT AAAAGAAGGA GGATTATGTG TAGCCTTGAA 1680 GGAGGAATGC TGTTTTTATG TGGATCATTC AGGGGCCATC AGAGACTCCA TGAACAAACT 1740 TAGAGAAAGG TTGGAGAAGC GTCGAAGGGA AAAGGAAACT ACTCAAGGGT GGTTTGAGGG 1800 ATGGTTCAAC AGGTCTCCTT GGTTGGCTAC CCTACTTTCT GCTTTAACAG GACCCTTAAT 1860 AGTCCTCCTC CTGTTACTCA CAGTTGGGCC ATGTATTATT AACAAGTTAA TTGCCTTCAT 1920 TAGAGAACGA ATAAGTGCAG TCCAGATCAT GGTACTTAGA CAACAGTACC AAAGCCCGTC 1980 TAGCAGGGAA GCTGGCCGCT AGCTCTACCA GTTCTAAGAT TAGAACTATT AACAAGAGAA 2040 GAAGTGGGGA ATGAAAGGAT GAAAATACAA CCTAAGCTAA TGAGAAGCTT AAAATTGTTC 2100 TGAATTCCAG AGTTTGTTCC TTATAGGTAA AAGATTAGGT TTTTTGCTGT TTTAAAATAT 2160 GCGGAAGTAA AATAGGCCCT GAGTACATGT CTCTAGGCAT GAAACTTCTT GAAACTATTT 2220 GAGATAACAA GAAAAGGGAG TTTCTAACTG CTTGTTTAGC TTCTGTAAAA CTGGTTGCGC 2280 CATAAAGATG TTGAAATGTT GATACACATA TCTTGGTGAC AACATGTCTC CCCCACCCCG 2340 AAACATGCGC AAATGTGTAA CTCTAAAACA ATTTAAATTA ATTGGTCCAC GAAGCGCGGG 2400 CTCTCGAAGT TTTAAATTGA CTGGTTTGTG ATATTTTGAA ATGATTGGTT TGTAAAGCGC 2460 GGGCTTTGCT GTGAACCCCA TAAAAGCTGT CCCGACTCCA CACTCGGGGC CGCAGTCCTC 2520 TACCCCTGCG TGGTGTACGA CTGTGGGCCC CAGCGCGCTT GGAATAAAAA TCCTCTTGCT 2580 GTTTGCATCA AGACCGCTTC TCGTGAGTGA TTAAGGGGAG TCGCCTTTTC CGAGCCTGGA 2640 GGTTCTTTTT GCTGGTCTTA CATTTGGGGG CTCGTCCGGG ATCTGTCGCG GCCACCCCTA 2700 ACACCCGAGA ACCGACTTGG AGGTAAAAAG GATCCTCTTT TTAACGTGTA TGCATGTACC 2760 GGCCGGCGTC TCTGTTCTGA GTGTCTGTTT TCAGTGGTGC GCGCTTTCGG TTTGCAGCTG 2820 TCCTCTCAGG CCGTAAGGGC TGGGGGACTG TGATCAGCAG ACGTGCTAGG AGGATCACAG 2880 GCTGCTGCCC TGGGGGACGC CCCGGGAGGT GAGGAGAGCC AGGGACGCCT GGTGGTCTCC 2940 TACTGTCGGT CAGAGGACCG AATTCTGTTG CTGAAGCGAA AGCTTCCCCC TCCGCGACCG 3000 TCCGACTCTT TTGCCTGCTT GTGGAATACG TGGACGGGTC ACGTGTGTCT GGATCTGTTG 3060 GTTTCTGTTT TGTGTGTCTT TGTCTTGTGT GTCCTTGTCT ACAGTTTTAA TATGGGACAG 3120 ACGGTGACGA CCCCTCTTAG TTTGACTCTC GACCATTGGA CTGAAGTTAA ATCCAGGGCT 3180 CATAATTTGT CAGTTCAGGT TAAGAAGGGA CCTTGGCAGA CTTTCTGTGT CTCTGAATGG 3240 CCGACATTCG ATGTTGGATG GCCATCAGAG GGGACCTTTA ATTCTGAGAT TATCCTGGCT 3300 GTTAAAGCAA TTATTTTTCA GACTGGACCC GGCTCTCATC CCGATCAGGA GCCCTATATC 3360 CTTACGTGGC AAGATTTGGC AGAGGATCCT CCGCCATGGG TTAAACCATG GCTGAATAAG 3420 CCAAGAAAGC CAGGTCCCCG AATTCTGGCT CTTGGAGAGA AAAACAAACA CTCGGCTGAA 3480 AAAGTCAAGC CCTCTCCTCA TATCTACCCC GAGATTGAGG AACCACCGGC TTGGCCGGAA 3540 CCCCAATCTG TTCCCCCACC CCCTTATCTG GCACAGGGTG CCGCGAGGGG ACCCTTTGCC 3600 CCTCCTGGAG CTCCGGCGGT GGAGGGACCT TCTGCAGGGA CTCGGAGCCG GAGGGGCGCC 3660 ACCCCGGAGC GGACAGACGA GATCGCGACA TTACCGCTGC GCACGTACGG CCCTCCCACA 3720 CCGGGGGGCC AATTGCAGCC CCTCCAGTAT TGGCCCTTTT CTTCTGCAGA TCTCTATAAT 3780 TGGAAAACTA ACCATCCCCC TTTCTCGGAG GATCCCCAAC GCCTCACGGG GTTGGTGGAG 3840 TCCCTTATGT TCTCTCACCA GCCTACTTGG GATGATTGTC AACAGCTGCT GCAGACACTC 3900 TTCACAACCG AGGAGCGAGA GAGAATTCTA TTAGAGGCTA GAAAAAATGT TCCTGGGGCC 3960 GACGGGCGAC CCACGCGGTT GCAAAATGAG ATTGACATGG GATTTCCCTT AACTCGCCCC 4020 GGTTGGGACT ACAACACGGC TGAAGGTAGG GAGAGCTTGA AAATCTATCG CCAGGCTCTG 4080 GTGGCGGGTC TCCGGGGCGC CTCAAGACGG CCCACTAATT TGGCTAAGGT AAGAGAAGTG 4140 ATGCAGGGAC CGAATGAACC CCCCTCTGTT TTTCTTGAGA GGCTCTTGGA AGCCTTCAGG 4200 CGGTACACCC CTTTTGATCC CACCTCAGAG GCCCAAAAAG CCTCAGTGGC TTTGGCCTTT 4260 ATAGGACAGT CAGCCTTGGA TATTAGAAAG AAGCTTCAGA GACTGGAAGG GTTACAGGAG 4320 GCTGAGTTAC GTGATCTAGT GAAGGAGGCA GAGAAAGTAT ATTACAAAAG GGAGACAGAA 4380 GAAGAAAGGG AACAAAGAAA AGAGAGAGAA AGAGAGGAAA GGGAGGAAAG ACGTAATAAA 4440 CGGCAAGAGA AGAATTTGAC TAAGATCTTG GCTGCAGTGG TTGAAGGGAA AAGCAATACG 4500 GAAAGAGAGA GAGATTTTAG GAAAATTAGG TCAGGCCCTA GACAGTCAGG GAACCTGGGC 4560 AATAGGACCC CACTCGACAA GGACCAATGT GCATATTGTA AAGAAAGAGG ACACTGGGCA 4620 AGGAACTGCC CCAAGAAGGG AAACAAAGGA CCAAGGATCC TAGCTCTAGA AGAAGATAAA 4680 GATTAGGGGA GACGGGGTTC GGACCCCCTC CCCGAGCCCA GGGTAACTTT GAAGGTGGAG 4740 GGGCAACCAG TTGAGTTCCT GGTTGATACC GGAGCGAAAC ATTCAGTGCT ACTACAGCCA 4800 TTAGGAAAAC TAAAAGATAA AAAATCCTGG GTGATGGGTG CACAGGGCAA CAACAGTATC 4860 CATGGACTAC CCGAAGACAG TTGACTTGGG AGTGGGACGG GTAACCCACT CGTTTCTGGT 4920 CATACCTGAG TGCCCAGCAC CCCTCTTAGG TAGAGACTTA TTGACCAAGA TGGGAGCACA 4980 AATTTCTTTT GAACAAGGGA AACCAGAAGT GTCTGCAAAT AACAAACCTA TCACTGTGTT 5040 GACCCTCCAA TTAGATGACG AATATCGACT ATACTCTCCC CTAGTAAAGC CTGATCAAAA 5100 TATACAATTC TGGTTGGAAC AGTTTCCCCA AGCCTGGGCA GAAACCGCAG GGATGGGTTT 5160 GGCAAAGCAA GTTCCCCCAC AAGTTATTCA ACTGAAGGCC AGTGCCACAC CAGTGTCAGT 5220 CAGACAGTAC CCCTTGAGTA AAGAAGCTCA AGAAGGAATT CGGCCGCATG TCCAAAGATT 5280 AATCCAACAG GGCATCCTAG TTCCTGTCCA ATCTCCCTGG AATACTCCCC TGCTACCGGT 5340 TAGAAAGCCT GGGACTAATG ACTATCGACC AGTACAGGAC TTGAGAGAGG TCAATAAACG 5400 GGTGCAGGAT ATACACCCAA CAGTCCCGAA CCCTTATAAC CTCTTGTGTG CTCTCCCACC 5460 CCAACGGAGC TGGTATACAG TATTGGACTT AAAGGATGCC TTCTTCTGCC TGAGATTACA 5520 CCCCACTAGC CAACCACTTT TTGCCTTCGA ATGGAGAGAT CCAGGTACGG GAAGAACCGG 5580 GCAGCTCACC TGGACCCGAC TGCCCCAAGG GTTCAAGAAC TCCCCGACCA TCTTTGACGA 5640 AGCCCTACAC AGAGACCTGG CCAACTTCAG GATCCAACAC CCTCAGGTGA CCCTCCTCCA 5700 GTACGTGGAT GACCTGCTTC TGGCGGGAGC CACCAAACAG GACTGCTTAG AAGGCACGAA 5760 GGCACTACTG CTGGAATTGT CTGACCTAGG CTACAGAGCC TCTGCTAAGA AGGCCCAGAT 5820 TTGCAGGAGA GAGGTAACAT ACTTGGGGTA CAGTTTACGG GACGGGCAGC GATGGCTGAC 5880 GGAGGCACGG AAGAAAACTG TAGTCCAGAT ACCGGCCCCA ACCACAGCCA AACAAATGAG 5940 AGAGTTTTTG GGGACAGCTG GATTTTGCAG ACTGTGGATC CCGGGGTTTG CGACCTTAGC 6000 AGCCCCACTC TACCCGCTAA CCAAAGAAAA AGGGGAATTC TCCTGGGCTC CTGAGCACCA 6060 GAAGGCATTT GATGCTATCA AAAAGGCCCT GCTGAGCGCA CCTGCTCTGG CCCTCCCTGA 6120 CGTAACTAAA CCCTTTACCC TTTATGTGGA TGAGCGTAAG GGAGTAGCCC GGGGAGTTTT 6180 AACCCAAACC CTAGGACCAT GGAGAAGACC TGTCGCCTAC CTGTCAAAGA AGCTCGATCC 6240 TGTAGCCAGT GGTTGGCCCA TATGCCTGAA GGCTATCGCA GCTGTGGCCA TACTGGTCAA 6300 GGACGCTGAC AAATTGACTT TGGGACAAGA ATATAACTGT AATAGCCCCC CATGCATTGG 6360 AGAACATCGT TCGGCAGCCC CCAGACCGAT GGATGACCAA CGCCCGCATG ACCCACTATC 6420 AAAGCCTGCT TCTCACAGAG AGGGTCACGT TCGCTCCACC AACCGCTCTC AACCCTGCCA 6480 CTCTTCTGCC TGAAGAGACT GATGAACCAG TGACTCATGA TTGCCATCAA CTATTGATTG 6540 AGGAGACTGG GGTCCGCAAG GACCTTACAG ACATACCGCT GACTGGAGAA GTGCTAACCT 6600 GGTTCACTGA CGGAAGCAGC TATGTGGTGG AAGGTAAGAG GATGGCTGGG GCGGCGGTGG 6660 TGGACGGGAC CCGCACGATC TGGGCCAGCA GCCTGCCGGG AGGAACTTCA GCACAAAAGG 6720 CTGAGCTCAT GGCCCTCACG CAAGCTTTGC GGCTGGCCGA AGGGAAATCC ATAAACATTT 6780 ATACGGACAG CAGGTATGCC TTTGCGACTG CACACGTACA TGGGGCCATC TATAAACAAA 6840 GGGGGTTGCT TACCTCAGCA GGGAGGGAAA TAAAGAACAA AGAGGAAATT CTAAGCCTAT 6900 TAGAAGCCGT ACATTTACCA AAAAGGCTAG CTATTATACA CTGTCCTGGA CATCAGAAAG 6960 CTAAAGATCT CATATCCAGA GGAAACCAGA TGGCTGACCG GGTTGCCAAG CAGGCAGCCC 7020 AGGGTGTTAA CCTTCTGCCT ATAATAGAAA TGCCCAAAGC CCCAGAACCC AGACGACAGT 7080 ACACCCTAGA AGACTGGCAA GAGATAAAAA AGATAGACCA TTCTCTGAGA CTCCGGAAGG 7140 GACCTGCTAT ACCTCAGATG GGAAGGAAAT CCTGCCCCAC AAAGAAGGGT TAGAATATGT 7200 CCAACAAGAT ACATCGTCTA ACCCACCTAG GAACTAAACA CCTGCAGCAG TTGGTCAGAA 7260 CATCCCCTTA TCATGTTCTG AGGCTACCAG GAGTGGCTGA CTCGGTGGTC AAACATTGTG 7320 TGCCCTGCCA GCTGGTTAAT GCTAATCCTT CCAGAATGCC TCCAGGGAAG AGACTAAGGG 7380 GAAGCCACCC AGGCGCTCAC TGGGAAGTGG ACTTCACTGA GGTAAAGCCG GCTAAATATG 7440 GAAACAAATA CCTATTGGTT TTTGTAGACA CCTTTTCAGG ATGGGTAGAG GCTTATCCTA 7500 CTAAGAAAGA GACTTCAACC GTGGTAGCTA AAAAAATACT GGAAGAAATT TTTCCAAGAT 7560 TTGGAATACC TAAGGTAATA GGGTCAGACA ATGGTCCAGC TTTTGTTGCC CAGGTAAGTC 7620 AGGGACTGGC CAAGATATTG GGGATTGATT GGAAACTGCA TTGTGCATAC AGACCCCAAA 7680 GCTCAGGACA GGTAGAGAGG ATGAATAGAA CCATTAAAGA GACCCTTACT AAATTGACCG 7740 CGGAGACTGG CGTTAATGAT TGGATAGCTC TCCTGCCCTT TGTGCTTTTT AGGGTTAGGA 7800 ACACCCCTGG ACAGTTTGGG CTGACCCCCT ATGAATTACT CTACGGGGGA CCCCCCCCAT 7860 TGGTAGAAAT TGCTTCTGTA CATAGTGCTG ATGTGCTGCT TTCCCAGCCT TTGTTCTCTA 7920 GGCTCAAGGC ACTTGAGTGG GTGAGACAAC GAGCGTGGAG GCAACTCCGG GAGGCCTACT 7980 CAGGAGGAGG AGACTTGCAG ATCCCACATC GTTTCCAAGT GGGAGATTCA GTCTACGTTA 8040 GACGCCACCG TGCAGGAAAC 8060 7333 base pairs nucleic acid single linear cDNA 2 CTACCCCTGC GTGGTGTACG ACTGTGGGCC CCAGCGCGCT TGGAATAAAA ATCCTCTTGC 60 TGTTTGCATC AAGACCGCTT CTTGTGAGTG ATTTGGGGTG TCGCCTCTTC CGAGCCCGGA 120 CGAGGGGGAT TGTTCTTTTA CTGGCCTTTC ATTTGGTGCG TTGGCCGGGA AATCCTGCGA 180 CCACCCCTTA CACCCGAGAA CCGACTTGGA GGTAAAGGGA TCCCCTTTGG AACATATGTG 240 TGTGTCGGCC GGCGTCTCTG TTCTGAGTGT CTGTTTTCGG TGATGCGCGC TTTCGGTTTG 300 CAGCTGTCCT CTCAGACCGT AAGGACTGGA GGACTGTGAT CAGCAGACGT GCTAGGAGGA 360 TCACAGGCTG CCACCCTGGG GGACGCCCCG GGAGGTGGGG AGAGCCAGGG ACGCCTGGTG 420 GTCTCCTACT GTCGGTCAGA GGACCGAGTT CTGTTGTTGA AGCGAAAGCT TCCCCCTCCG 480 CGGCCGTCCG ACTCTTTTGC CTGCTTGTGG AAGACGCGGA CGGGTCGCGT GTGTCTGGAT 540 CTGTTGGTTT CTGTTTCGTG TGTCTTTGTC TTGTGCGTCC TTGTCTACAG TTTTAATATG 600 GGACAGACAG TGACTACCCC CCTTAGTTTG ACTCTCGACC ATTGGACTGA AGTTAGATCC 660 AGGGCTCATA ATTTGTCAGT TCAGGTTAAG AAGGGACCTT GGCAGACTTT CTGTGCCTCT 720 GAATGGCCAA CATTCGATGT TGGATGGCCA TCAGAGGGGA CCTTTAATTC TGAAATTATC 780 CTGGCTGTTA AGGCAATCAT TTTTCAGACT GGACCCGGCT CTCATCCTGA TCAGGAGCCC 840 TATATCCTTA CGTGGCAAGA TTTGGCAGAA GATCCTCCGC CATGGGTTAA ACCATGGCTA 900 AATAAACCAA GAAAGCCAGG TCCCCGAATC CTGGCTCTTG GAGAGAAAAA CAAACACTCG 960 GCCGAAAAAG TCGAGCCCTC TCCTCGTATC TACCCCGAGA TCGAGGAGCC GCCGACTTGG 1020 CCGGAACCCC AACCTGTTCC CCCACCCCCT TATCCAGCAC AGGGTGCTGT GAGGGGACCC 1080 TCTGCCCCTC CTGGAGCTCC GGTGGTGGAG GGACCTGCTG CCGGGACTCG GAGCCGGAGA 1140 GGCGCCACCC CGGAGCGGAC AGACGAGATC GCGATATTAC CGCTGCGCAC CTATGGCCCT 1200 CCCATGCCAG GGGGCCAATT GCAGCCCCTC CAGTATTGGC CCTTTTCTTC TGCAGATCTC 1260 TATAATTGGA AAACTAACCA TCCCCCTTTC TCGGAGGATC CCCAACGCCT CACGGGGTTG 1320 GTGGAGTCCC TTATGTTCTC TCACCAGCCT ACTTGGGATG ATTGTCAACA GCTGCTGCAG 1380 ACACTCTTCA CAACCGAGGA GCGAGAGAGA ATTCTGTTAG AGGCTAAAAA AAATGTTCCT 1440 GGGGCCGACG GGCGACCCAC GCAGTTGCAA AATGAGATTG ACATGGGATT TCCCTTGACT 1500 CGCCCCGGTT GGGACTACAA CACGGCTGAA GGTAGGGAGA GCTTGAAAAT CTATCGCCAG 1560 GCTCTGGTGG CGGGTCTCCG GGGCGCCTCA AGACGGCCCA CTAATTTGGC TAAGGTAAGA 1620 GAGGTGATGC AGGGACCGAA CGAACCTCCC TCGGTATTTC TTGAGAGGCT CATGGAAGCC 1680 TTCAGGCGGT TCACCCCTTT TGATCCTACC TCAGAGGCCC AGAAAGCCTC AGTGGCCCTG 1740 GCCTTCATTG GGCAGTCGGC TCTGGATATC AGGAAGAAAC TTCAGAGACT GGAAGGGTTA 1800 CAGGAGGCTG AGTTACGTGA TCTAGTGAGA GAGGCAGAGA AGGTGTATTA CAGAAGGGAG 1860 ACAGAAGAGG AGAAGGAACA GAGAAAAGAA AAGGAGAGAG AAGAAAGGGA GGAAAGACGT 1920 GATAGACGGC AAGAGAAGAA TTTGACTAAG ATCTTGGCCG CAGTGGTTGA AGGGAAGAGC 1980 AGCAGGGAGA GAGAGAGAGA TTTTAGGAAA ATTAGGTCAG GCCCTAGACA GTCAGGGAAC 2040 CTGGGCAATA GGACCCCACT CGACAAGGAC CAGTGTGCGT ATTGTAAAGA AAAAGGACAC 2100 TGGGCAAGGA ACTGCCCCAA GAAGGGAAAC AAAGGACCGA AGGTCCTAGC TCTAGAAGAA 2160 GATAAAGATT AGGGGAGACG GGGTTCGGAC CCCCTCCCCG AGCCCAGGGT AACTTTGAAG 2220 GTGGAGGGGC AACCAGTTGA GTTCCTGGTT GATACCGGAG CGGAGCATTC AGTGCTGCTA 2280 CAACCATTAG GAAAACTAAA AGAAAAAAAA TCCTGGGTGA TGGGTGCCAC AGGGCAACGG 2340 CAGTATCCAT GGACTACCCG AAGAACCGTT GACTTGGGAG TGGGACGGGT AACCCACTCG 2400 TTTCTGGTCA TCCCTGAGTG CCCAGTACCC CTTCTAGGTA GAGACTTACT GACCAAGATG 2460 GGAGCTCAAA TTTCTTTTGA ACAAGGAAGA CCAGAAGTGT CTGTGAATAA CAAACCCATC 2520 ACTGTGTTGA CCCTCCAATT AGATGATGAA TATCGACTAT ATTCTCCCCA AGTAAAGCCT 2580 GATCAAGATA TACAGTCCTG GTTGGAGCAG TTTCCCCAAG CCTGGGCAGA AACCGCAGGG 2640 ATGGGTTTGG CAAAGCAAGT TCCCCCACAG GTTATTCAAC TGAAGGCCAG TGCTACACCA 2700 GTATCAGTCA GACAGTACCC CTTGAGTAGA GAGGCTCGAG AAGGAATTTG GCCGCATGTT 2760 CAAAGATTAA TCCAACAGGG CATCCTAGTT CCTGTCCAAT CCCCTTGGAA TACTCCCCTG 2820 CTACCGGTTA GGAAGCCTGG GACCAATGAT TATCGACCAG TACAGGACTT GAGAGAGGTC 2880 AATAAAAGGG TGCAGGACAT ACACCCAACG GTCCCGAACC CTTATAACCT CTTGAGCGCC 2940 CTCCCGCCTG AACGGAACTG GTACACAGTA TTGGACTTAA AAGATGCCTT CTTCTGCCTG 3000 AGATTACACC CCACTAGCCA ACCACTTTTT ACCTTCGAAT GGAGAGATCC AGGTACGGGA 3060 AGAACCGGGC AGCTCACCTG GACCCGACTG CCCCAAGGGT TCAAGAACTC CCCGACCATC 3120 TTTGACGAAG CCCTACACAG GGACCTGGCC AACTTCAGGA TCCAACACCC TCAGGTGACC 3180 CTCCTCCAGT ACGTGGATGA CCTGCTTCTG GCGGGAGCCA CCAAACAGGA CTGCTTAGAA 3240 GGTACGAAGG CACTACTGCT GGAATTGTCT GACCTAGGCT ACAGAGCCTC TGCTAAGAAG 3300 GCCCAGATTT GCAGGAGAGA GGTAACATAC TTGGGGTACA GTTTGCGGGG CGGGCAGCGA 3360 TGGCTGACGG AGGCACGGAA GAAAACTGTA GTCCAGATAC CGGCCCCAAC CACAGCCAAA 3420 CAAGTGAGAG AGTTTTTGGG GACAGCTGGA TTTTGCAGAC TGTGGATCCC GGGGTTTGCG 3480 ACCTTAGCAG CCCCACTCTA CCCGCTAACC AAAGAAAAAG GGGGTTGCTT ACCTCAGCAG 3540 GGAGGGAAAT AAAGAACAAA GAGGAAATTC TAAGCCTATT AGAAGCCTTA CATTTGCCAA 3600 AAAGGCTAGC TATTATACAC TGTCCTGGAC ATCAGAAAGC CAAAGATCTC ATATCTAGAG 3660 GGAACCAGAT GGCTGACCGG GTTGCCAAGC AGGCAGCCCA GGCTGTTAAC CTTCTGCCTA 3720 TAATAGAAAC GCCCAAAGCC CCAGAACCCA GACGACAGTA CACCCTAGAA GACTGGCAAG 3780 AGATAAAAAA GATAGACCAG TTCTCTGAGA CTCCGGAGGG GACCTGCTAT ACCTCATATG 3840 GGAAGGAAAT CCTGCCCCAC AAAGAAGGGT TAGAATATGT CCAACAGATA CATCGTCTAA 3900 CCCACCTAGG AACTAAACAC CTGCAGCAGT TGGTCAGAAC ATCCCCTTAT CATGTTCTGA 3960 GGCTACCAGG AGTGGCTGAC TCGGTGGTCA AACATTGTGT GCCCTGCCAG CTGGTTAATG 4020 CTAATCCTTC CAGAATACCT CCAGGAAAGA GACTAAGGGG AAGCCACCCA GGCGCTCACT 4080 GGGAAGTGGA CTTCACTGAG GTAAAGCCGG CTAAATACGG AAACAAATAT CTATTGGTTT 4140 TTGTAGACAC CTTTTCAGGA TGGGTAGAGG CTTATCCTAC TAAAAAAGAG ACTTCAACCG 4200 TGGTGGCTAA GAAAATACTG GAGGAAATTT TTCCAAGATT TGGAATACCT AAGGTAATAG 4260 GGTCAGACAA TGGTCCAGCT TTCGTTGCCC AGGTAAGTCA GGGACTGGCC AAGATATTGG 4320 GGATTGATTG AAAACTGCAT TGTGCATACA GACCCCAAAG CTCAGGACAG GTAGAGAGGA 4380 TGAATAGAAC CATTAAAGAG ACCCTTACCA AATTGACCAC AGAGACTGGC ATTAATGATT 4440 GGATGGCTCT CCTGCCCTTT GTGCTTTTTA GGGTGAGGAA CACCCCTGGA CAGTTTGGGC 4500 TGACCCCCTA TAAATTGCTC TACGGGGGAC CCCCCCCGTT GGCAGAAATT GCCTTTGCAC 4560 ATAGTGCTGA TGTGCTGCTT TCCCAGCCTT TGTTCTCTAG GCTCAAGGCG CTCGAGTGGG 4620 TGAGGCAGCG AGCGTGGAAG CAGCTCCGGG AGGCCTACTC AGGAGGAGAC TTGCAAGTTC 4680 CACATCGCTT CCAAGTTGGA GATTCAGTCT ATGTTAGACG CCACCGTGCA GGAAACCTCG 4740 AGACTCGGTA GAAGGGACCT TATCTCGTAC TTTTGACCAC ACCAACGGCT GTGAAAGTCG 4800 AAGGAATCCC CTTAAGCTTC GCCTCCATCG CGTGGTTCCT TACTCTGTCA ATAACTCCTC 4860 AAGTTAATGG TAAACGCCTT GTGGACAGCC CGAACTCCCA TAAACCCTTA TCTCTCACCT 4920 GGTTACTTAC TGACTCCGGT ACAGGTATTA ATATTAACAG CACTCAAGGG GAGGCTCCCT 4980 TGGGGACCTG GTGGCCTGAA TTATATGTCT GCCTTCGATC AGTAATCCCT GGTCTCAATG 5040 ACCAGGCCAC ACCCCCCGAT GTACTCCGTG CTTACGGGTT TTACGTTTGC CCAGGACCCC 5100 CAAATAATGA AGAATATTGT GGAAATCCTC AGGATTTCTT TTGCAAGCAA TGGAGCTGCA 5160 TAACTTCTAA TGATGGGAAT TGGAAATGGC CAGTCTCTCA GCAAGACAGA GTAAGTTACT 5220 CTTTTGTTAA CAATCCTACC AGTTATAATC AATTTAATTA TGGCCATGGG AGATGGAAAG 5280 ATTGGCAACA GCGGGTACAA AAAGATGTAC GAAATAAGCA AATAAGCTGT CATTCGTTAG 5340 ACCTAGATTA CTTAAAAATA AGTTTCACTG AAAAAGGAAA ACAAGAAAAT ATTCAAAAGT 5400 GGGTAAATGG TATATCTTGG GGAATAGTGT ACTATGGAGG CTCTGGGAGA AAGAAAGGAT 5460 CTGTTCTGAC TATTCGCCTC AGAATAGAAA CTCAGATGGA ACCTCCGGTT GCTATAGGAC 5520 CAAATAAGGG TTTGGCCGAA CAAGGACCTC CAATCCAAGA ACAGAGGCCA TCTCCTAACC 5580 CCTCTGATTA CAATACAACC TCTGGATCAG TCCCCACTGA GCCTAACATC ACTATTAAAA 5640 CAGGGGCGAA ACTTTTTAGC CTCATCCAGG GAGCTTTTCA AGCTCTTAAC TCCACGACTC 5700 CAGAGGCTAC CTCTTCTTGT TGGCTTTGCT TAGCTTCGGG CCCACCTTAC TATGAGGGAA 5760 TGGCTAGAGG AGGGAAATTC AATGTGACAA AGGAACATAG AGACCAATGT ACATGGGGAT 5820 CCCAAAATAA GCTTACCCTT ACTGAGGTTT CTGGAAAAGG CACCTGCATA GGGATGGTTC 5880 CCCCATCCCA CCAACACCTT TGTAACCACA CTGAAGCCTT TAATCGAACC TCTGAGAGTC 5940 AATATCTGGT ACCTGGTTAT GACAGGTGGT GGGCATGTAA TACTGGATTA ACCCCTTGTG 6000 TTTCCACCTT GGTTTTCAAC CAAACTAAAG ACTTTTGCGT TATGGTCCAA ATTGTCCCCC 6060 GGGTGTACTA CTATCCCGAA AAAGCAGTCC TTGATGAATA TGACTATAGA TATAATCGGC 6120 CAAAAAGAGA GCCCATATCC CTGACACTAG CTGTAATGCT CGGATTGGGA GTGGCTGCAG 6180 GCGTGGGAAC AGGAACGGCT GCCCTAATCA CAGGACCGCA ACAGCTGGAG AAAGGACTTA 6240 GTAACCTACA TCGAATTGTA ACGGAAGATC TCCAAGCCCT AGAAAAATCT GTCAGTAACC 6300 TGGAGGAATC CCTAACCTCC TTATCTGAAG TGGTTCTACA GAACAGAAGG GGGTTAGATC 6360 TGTTATTTCT AAAAGAAGGA GGGTTATGTG TAGCCTTAAA AGAGGAATGC TGCTTCTATG 6420 TAGATCACTC AGGAGCCATC AGAGACTCCA TGAGCAAGCT TAGAGAAAGG TTAGAGAGGC 6480 GTCGAAGGGA AAGAGAGGCT GACCAGGGGT GGTTTGAAGG ATGGTTCAAC AGGTCTCCTT 6540 GGATGACCAC CCTGCTTTCT GCTCTGACGG GGCCCCTAGT AGTCCTGCTC CTGTTACTTA 6600 CAGTTGGGCC TTGCTTAATT AATAGGTTTG TTGCCTTTGT TAGAGAACGA GTGAGTGCAG 6660 TCCAGATCAT GGTACTTAGG CAACAGTACC AAGGCCTTCT GAGCCAAGGA GAAACTGACC 6720 TCTAGCCTTC CCAGTTCTAA GATTAGAACT ATTAACAAGA CAAGAAGTGG GGAATGAAAG 6780 GATGAAAATG CAACCTAACC CTCCCAGAAC CCAGGAAGTT AATAAAAAGC TCTAAATGCC 6840 CCCGAATTCC AGACCCTGCT GGCTGCCAGT AAATAGGTAG AAGGTCACAC TTCCTATTGT 6900 TCCAGGGCCT GCTATCCTGG CCTAAGTAAG ATAACAGGAA ATGAGTTGAC TAATCGCTTA 6960 TCTGGATTCT GTAAAACTGA CTGGCACCAT AGAAGAATTG ATTACACATT GACAGCCCTA 7020 GTGACCTATC TCAACTGCAA TCTGTCACTC TGCCCAGGAG CCCACGCAGA TGCGGACCTC 7080 CGGAGCTATT TTAAAATGAT TGGTCCACGG AGCGCGGGCT CTCGATATTT TAAAATGATT 7140 GGTCCATGGA GCGCGGGCTC TCGATATTTT AAAATGATTG GTTTGTGACG CACAGGCTTT 7200 GTTGTGAACC CCATAAAAGC TGTCCCGATT CCGCACTCGG GGCCGCAGTC CTCTACCCCT 7260 GCGTGGTGTA CGACTGTGGG CCCCAGCGCG CTTGGAATAA AAATCCTCTT GCTGTTTGCA 7320 TCAAAAAAAA AAA 7333 8132 base pairs nucleic acid single linear cDNA 3 GCGTGGTGTA CGACTGTGGG CCCCAGCGCG CTTGGAATAA AAATCCTCTT GCTGTTTGCA 60 TCAAGACCGC TTCTCGTGAG TGATTAAGGG GAGTCGCCTT TTCCGAGCCT GGAGGTTCTT 120 TTTGCTGGTC TTACATTTGG GGGCTCGTCC GGGATCTGTC GCGGCCACCC CTAACACCCG 180 AGAACCGACT TGGAGGTAAA AAGGATCCTC TTTTTAACGT GTATGCATGT ACCGGCCGGC 240 GTCTCTGTTC TGAGTGTCTG TTTTCAGTGG TGCGCGCTTT CGGTTTGCAG CTGTCCTCTC 300 AGGCCGTAAG GGCTGGGGGA CTGTGATCAG CAGACGTGCT AGGAGGATCA CAGGCTGCTG 360 CCCTGGGGGA CGCCCCGGGA GGTGAGGAGA GCCAGGGACG CCTGGTGGTC TCCTACTGTC 420 GGTCAGAGGA CCGAATTCTG TTGCTGAAGC GAAAGCTTCC CCCTCCGCGA CCGTCCGACT 480 CTTTTGCCTG CTTGTGGAAG ACGTGGACGG GTCACGTGTG TCTGGATCTG TTGGTTTCTG 540 TTTTGTGTGT CTTTGTCTTG TGTGTCCTTG TCTACAGTTT TAATATGGGA CAGACGGTGA 600 CGACCCCTCT TAGTTTGACT CTCGACCATT GGACTGAAGT TAAATCCAGG GCTCATAATT 660 TGTCAGTTCA GGTTAAGAAG GGACCTTGGC AGACTTTCTG TGTCTCTGAA TGGCCGACAT 720 TCGATGTTGG ATGGCCATCA GAGGGGACCT TTAATTCTGA GATTATCCTG GCTGTTAAAG 780 CAGTTATTTT TCAGACTGGA CCCGGCTCTC ATCCCGATCA GGAGCCCTAT ATCCTTACGT 840 GGCAAGATTT GGCAGAGGAT CCTCCGCCAT GGGTTAAACC ATGGCTGAAT AAGCCAAGAA 900 AGCCAGGTCC CCGAATTCTG GCTCTTGGAG AGAAAAACAA ACACTCGGCT GAAAAAGTCA 960 AGCCCTCTCC TCATATCTAC CCCGAGATTG AGGAGCCACC GGCTTGGCCG GAACCCCAAT 1020 CTGTTCCCCC ACCCCCTTAT CTGGCACAGG GTGCCGCGAG GGGACCCTTT GCCCCTCCTG 1080 GAGCTCCGGC GGTGGAGGGA CCTGCTGCAG GGACTCGGAG CCGGAGGGGC GCCACCCCGG 1140 AGCGGACAGA CGAGATCGCG ACATTACCGC TGCGCACGTA CGGCCCTCCC ACACCGGGGG 1200 GCCAATTGCA GCCCCTCCAG TATTGGCCCT TTTCTTCTGC AGATCTCTAT AATTGGAAAA 1260 CTAACCATCC CCCTTTCTCG GAGGATCCCC AACGCCTCAC GGGGTTGGTG GAGTCCCTTA 1320 TGTTCTCTCA CCAGCCTACT TGGGATGATT GTCAACAGCT GCTGCAGACA CTCTTCACAA 1380 CCGAGGAGCG AGAGAGAATT CTATTAGAGG CTAGAAAAAA TGTTCCTGGG GCCGACGGGC 1440 GACCCACGCG GTTGCAAAAT GAGATTGACA TGGGATTTCC CTTAACTCGC CCCGGTTGGG 1500 ACTACAACAC GGCTGAAGGT AGGGAGAGCT TGAAAATCTA TCGCCAGGCT CTGGTGGCGG 1560 GTCTCCGGGG CGCCTCAAGA CGGCCCACTA ATTTGGCTAA GGTAAGAGAA GTGATGCAGG 1620 GACCGAATGA ACCCCCCTCT GTTTTTCTTG AGAGGCTCTT GGAAGCCTTC AGGCGGTACA 1680 CCCCTTTTGA TCCCACCTCA GAGGCCCAAA AAGCCTCAGT GGCTTTGGCC TTTATAGGAC 1740 AGTCAGCCTT GGATATTAGA AAGAAGCTTC AGAGACTGGA AGGGTTACAG GAGGCTGAGT 1800 TACGTGATCT AGTGAAGGAG GCAGAGAAAG TATATTACAA AAGGGAGACA GAAGAAGAAA 1860 GGGAACAAAG AAAAGAGAGA GAAAGAGAGG AAAGGGAGGA AAGACGTAAT AAACGGCAAG 1920 AGAAGAATTT GACTAAGATC TTGGCTGCAG TGGTTGAAGG GAAAAGCAAT ACGGAAAGAG 1980 AGAGAGATTT TAGGAAAATT AGGTCAGGCC CTAGACAGTC AGGGAACCTG GGCAATAGGA 2040 CCCCACTCGA CAAGGACCAA TGTGCATATT GTAAAGAAAG AGGACACTGG GCAAGGAACT 2100 GCCCCAAGAA GGGAAACAAA GGACCAAGGA TCCTAGCTCT AGAAGAAGAT AAAGATTAGG 2160 GGAGACGGGG TTCGGACCCC CTCCCCGAGC CCAGGGTAAC TTTGAAGGTG GAGGGGCAAC 2220 CAGTTGAGTT CCTGGTTGAT ACCGGAGCGA AACATTCAGT GCTACTACAG CCATTAGGAA 2280 AACTAAAAGA TAAAAAATCC TGGGTGATGG GTGCCACAGG GCAACAACAG TATCCATGGA 2340 CTACCCGAAG AACAGTTGAC TTGGGAGTGG GACGGGTAAC CCACTCGTTT CTGGTCATAC 2400 CTGAGTGCCC AGCACCCCTC TTAGGTAGAG ACTTATTGAC CAAGATGGGA GCACAAATTT 2460 CTTTTGAACA AGGGAAACCA GAAGTGTCTG CAAATAACAA ACCTATCACT GTGTTGACCC 2520 TCCAATTAGA TGACGAATAT CGACTATACT CTCCCCTAGT AAAGCCTGAT CAAAATATAC 2580 AATTCTGGTT GGAACAGTTT CCCCAAGCCT GGGCAGAAAC CGCAGGGATG GGTTTGGCAA 2640 AGCAAGTTCC CCCACAAGTT ATTCAACTGA AGGCCAGTGC CACACCAGTG TCAGTCAGAC 2700 AGTACCCCTT GAGTAAAGAA GCTCAAGAAG GAATTCGGCC GCATGTCCAA AGATTAATCC 2760 AACAGGGCAT CCTAGTTCCT GTCCAATCTC CCTGGAATAC TCCCCTGCTA CCGGTTAGAA 2820 AGCCTGGGAC TAATGACTAT CGACCAGTAC AGGACTTGAG AGAGGTCAAT AAACGGGTGC 2880 AGGATATACA CCCAACAGTC CCGAACCCTT ATAACCTCTT GTGTGCTCTC CCACCCCAAC 2940 GGAGCTGGTA TACAGTATTG GACTTAAAGG ATGCCTTCTT CTGCCTGAGA TTACACCCCA 3000 CTAGCCAACC ACTTTTTGCC TTCGAATGGA GAGATCCAGG TACGGGAAGA ACCGGGCAGC 3060 TCACCTGGAC CCGACTGCCC CAAGGGTTCA AGAACTCCCC GACCATCTTT GACGAAGCCC 3120 TACACAGAGA CCTGGCCAAC TTCAGGATCC AACACCCTCA GGTGACCCTC CTCCAGTACG 3180 TGGATGACCT GCTTCTGGCG GGAGCCACCA AACAGGACTG CTTAGAAGGC ACGAAGGCAC 3240 TACTGCTGGA ATTGTCTGAC CTAGGCTACA GAGCCTCTGC TAAGAAGGCC CAGATTTGCA 3300 GGAGAGAGGT AACATACTTG GGGTACAGTT TGCGGGACGG GCAGCGATGG CTGACGGAGG 3360 CACGGAAGAA AACTGTAGTC CAGATACCGG CCCCAACCAC AGCCAAACAA ATGAGAGAGT 3420 TTTTGGGGAC AGCTGGATTT TGCAGACTGT GGATCCCGGG GTTTGCGACC TTAGCAGCCC 3480 CACTCTACCC GCTAACCAAA GAAAAAGGGG AATTCTCCTG GGCTCCTGAG CACCAGAAGG 3540 CATTTGATGC TATCAAAAAG GCCCTGCTGA GCGCACCTGC TCTGGCCCTC CCTGACGTAA 3600 CTAAACCCTT TACCCTTTAT GTGGATGAGC GTAAGGGAGT AGCCCGGGGA GTTTTAACCC 3660 AAACCCTAGG ACCATGGAGA AGACCTGTCG CCTACCTGTC AAAGAAGCTC GATCCTGTAG 3720 CCAGTGGTTG GCCCATATGC CTGAAGGCTA TCGCAGCTGT GGCCATACTG GTCAAGGACG 3780 CTGACAAATT GACTTTGGGA CAGAATATAA CTGTAATAGC CCCCCATGCA TTGGAGAACA 3840 TCGTTCGGCA GCCCCCAGAC CGATGGATGA CCAACGCCCG CATGACCCAC TATCAAAGCC 3900 TGCTTCTCAC AGAGAGGGTC ACGTTCGCTC CACCAGCCGC TCTCAACCCT GCCACTCTTC 3960 TGCCTGAAGA GACTGATGAA CCAGTGACTC ATGATTGCCA TCAACTATTG ATTGAGGAGA 4020 CTGGGGTCCG CAAGGACCTT ACAGACATAC CGCTGACTGG AGAAGTGCTA ACCTGGTTCA 4080 CTGACGGAAG CAGCTATGTG GTGGAAGGTA AGAGGATGGC TGGGGCGGCG GTGGTGGACG 4140 GGACCCGCAC GATCTGGGCC AGCAGCCTGC CGGAAGGAAC TTCAGCACAA AAGGCTGAGC 4200 TCATGGCCCT CACGCAAGCT TTGCGGCTGG CCGAAGGGAA ATCCATAAAC ATTTATACGG 4260 ACAGCAGGTA TGCCTTTGCG ACTGCACACG TACATGGGGC CATCTATAAA CAAAGGGGGT 4320 TGCTTACCTC AGCAGGGAGG GAAATAAAGA ACAAAGAGGA AATTCTAAGC CTATTAGAAG 4380 CCGTACATTT ACCAAAAAGG CTAGCTATTA TACACTGTCC TGGACATCAG AAAGCTAAAG 4440 ATCTCATATC CAGAGGAAAC CAGATGGCTG ACCGGGTTGC CAAGCAGGCA GCCCAGGGTG 4500 TTAACCTTCT GCCTATAATA GAAATGCCCA AAGCCCCAGA ACCCAGACGA CAGTACACCC 4560 TAGAAGACTG GCAAGAGATA AAAAAGATAG ACCAGTTCTC TGAGACTCCG GAAGGGACCT 4620 GCTATACCTC AGATGGGAAG GAAATCCTGC CCCACAAAGA AGGGTTAGAA TATGTCCAAC 4680 AGATACATCG TCTAACCCAC CTAGGAACTA AACACCTGCA GCAGTTGGTC AGAACATCCC 4740 CTTATCATGT TCTGAGGCTA CCAGGAGTGG CTGACTCGGT GGTCAAACAT TGTGTGCCCT 4800 GCCAGCTGGT TAATGCTAAT CCTTCCAGAA TGCCTCCAGG GAAGAGACTA AGGGGAAGCC 4860 ACCCAGGCGC TCACTGGGAA GTGGACTTCA CTGAGGTAAA GCCGGCTAAA TACGGAAACA 4920 AATACCTATT GGTTTTTGTA GACACCTTTT CAGGATGGGT AGAGGCTTAT CCTACTAAGA 4980 AAGAGACTTC AACCGTGGTG GCTAAAAAAA TACTGGAAGA AATTTTTCCA AGATTTGGAA 5040 TACCTAAGGT AATAGGGTCA GACAATGGTC CAGCTTTTGT TGCCCAGGTA AGTCAGGGAC 5100 TGGCCAAGAT ATTGGGGATT GATTGGAAAC TGCATTGTGC ATACAGACCC CAAAGCTCAG 5160 GACAGGTAGA GAGGATGAAT AGAACCATTA AAGAGACCCT TACTAAATTG ACCGCGGAGA 5220 CTGGCGTTAA TGATTGGATA GCTCTCCTGC CCTTTGTGCT TTTTAGGGTT AGGAACACCC 5280 CTGGACAGTT TGGGCTGACC CCCTATGAAT TACTCTACGG GGGACCCCCC CCATTGGTAG 5340 AAATTGCTTC TGTACATAGT GCTGACGTGC TGCTTTCCCA GCCTTTGTTC TCTAGGCTCA 5400 AGGCACTTGA GTGGGTGAGA CAACGAGCGT GGAGGCAACT CCGGGAGGCC TACTCAGGAG 5460 GAGGAGACTT GCAGATCCCA CATCGTTTCC AAGTGGGAGA TTCAGTCTAC GTTAGACGCC 5520 ACCGTGCAGG AAACCTCGAG ACTCGGTGGA AGGGCCCTTA TCTCGTACTT TTGACCACAC 5580 CAACGGCTGT GAAAGTCGAA GGAATCTCCA CCTGGATCCA TGCATCCCAC GTTAAACCGG 5640 CGCCACCTCC CGATTCGGGG TGGAAAGCCG AAAAGACTGA AAATCCCCTT AAGCTTCGCC 5700 TCCATCGCGT GGTTCCTTAC TCTGTCAATA ACCTCTCAGA CTAATGGTAT GCGCATAGGA 5760 GACAGCCTGA ACTCCCATAA ACCCTTATCT CTCACCTGGT TAATTACTGA CTCCGGCACA 5820 GGTATTAATA TCAACAACAC TCAAGGGGAG GCTCCTTTAG GAACCTGGTG GCCTGATCTA 5880 TACGTTTGCC TCAGATCAGT TATTCCTAGT CTGACCTCAC CCCCAGATAT CCTCCATGCT 5940 CACGGATTTT ATGTTTGCCC AGGACCACCA AATAATGGAA AACATTGCGG AAATCCCAGA 6000 GATTTCTTTT GTAAACAATG GAACTGTGTA ACCTCTAATG ATGGATATTG GAAATGGCCA 6060 ACCTCTCAGC AGGATAGGGT AAGTTTTTCT TATGTCAACA CCTATACCAG CTCTGGACAA 6120 TTTAATTACC TGACCTGGAT TAGAACTGGA AGCCCCAAGT GCTCTCCTTC AGACCTAGAT 6180 TACCTAAAAA TAAGTTTCAC TGAGAAAGGA AAACAAGAAA ATATCCTAAA ATGGGTAAAT 6240 GGTATGTCTT GGGGAATGGT ATATTATGGA GGCTCGGGTA AACAACCAGG CTCCATTCTA 6300 ACTATTCGCC TCAAAATAAA CCAGCTGGAG CCTCCAATGG CTATAGGACC AAATACGGTC 6360 TTGACGGGTC AAAGACCCCC AACCCAAGGA CCAGGACCAT CCTCTAACAT AACTTCTGGA 6420 TCAGACCCCA CTGAGTCTAA CAGCACGACT AAAATGGGGG CAAAACTTTT TAGCCTCATC 6480 CAGGGAGCTT TTCAAGCTCT TAACTCCACG ACTCCAGAGG CTACCTCTTC TTGTTGGCTA 6540 TGCTTAGCTT CGGGCCCACC TTACTATGAA GGAATGGCTA GAAGAGGGAA ATTCAATGTG 6600 ACAAAAGAAC ATAGAGACCA ATGCACATGG GGATCCCAAA ATAAGCTTAC CCTTACTGAG 6660 GTTTCTGGAA AAGGCACCTG CATAGGAAAG GTTCCCCCAT CCCACCAACA CCTTTGTAAC 6720 CACACTGAAG CCTTTAATCA AACCTCTGAG AGTCAATATC TGGTACCTGG TTATGACAGG 6780 TGGTGGGCAT GTAATACTGG ATTAACCCCT TGTGTTTCCA CCTTGGTTTT TAACCAAACT 6840 AAAGATTTTT GCATTATGGT CCAAATTGTT CCCCGAGTGT ATTACTATCC CGAAAAAGCA 6900 ATCCTTGATG AATATGACTA CAGAAATCAT CGACAAAAGA GAGAACCCAT ATCTCTGACA 6960 CTTGCTGTGA TGCTCGGACT TGGAGTGGCA GCAGGTGTAG GAACAGGAAC AGCTGCCCTG 7020 GTCACGGGAC CACAGCAGCT AGAAACAGGA CTTAGTAACC TACATCGAAT TGTAACAGAA 7080 GATCTCCAAG CCCTAGAAAA ATCTGTCAGT AACCTGGAGG AATCCCTAAC CTCCTTATCT 7140 GAAGTAGTCC TACAGAATAG AAGAGGGTTA GATTTATTAT TTCTAAAAGA AGGAGGATTA 7200 TGTGTAGCCT TGAAGGAGGA ATGCTGTTTT TATGTGGATC ATTCAGGGGC CATCAGAGAC 7260 TCCATGAACA AGCTTAGAGA AAGGTTGGAG AAGCGTCGAA GGGAAAAGGA AACTACTCAA 7320 GGGTGGTTTG AGGGATGGTT CAACAGGTCT CTTTGGTTGG CTACCCTACT TTCTGCTTTA 7380 ACAGGACCCT TAATAGTCCT CCTCCTGTTA CTCACAGTTG GGCCATGTAT TATTAACAAG 7440 TTAATTGCCT TCATTAGAGA ACGAATAAGT GCAGTCCAGA TCATGGTACT TAGACAACAG 7500 TACCAAAGCC CGTCTAGCAG GGAAGCTGGC CGCTAGCTCT ACCAGTTCTA AGATTAGAAC 7560 TATTAACAAG AGAAGAAGTG GGGAATGAAA GGATGAAAAT ACAACCTAAG CTAATGAGAA 7620 GCTTAAAATT GTTCTGAATT CCAGAGTTTG TTCCTTATAG GTAAAAGATT AGGTTTTTTG 7680 CTGTTTTAAA ATATGCGGAA GTAAAATAGG CCCTGAGTAC ATGTCTCTAG GCATGAAACT 7740 TCTTGAAACT ATTTGAGATA ACAAGAAAAG GGAGTTTCTA ACTGCTTGTT TAGCTTCTGT 7800 AAAACTGGTT GCGCCATAAA GATGTTGAAA TGTTGATACA CATATCTTGG TGACAACATG 7860 TCTCCCCCAC CCCGAAACAT GCGCAAATGT GTAACTCTAA AACAATTTAA ATTAATTGGT 7920 CCACGAAGCG CGGGCTCTCG AAGTTTTAAA TTGACTGGTT TGTGATATTT TGAAATGATT 7980 GGTTTGTAAA GCGCGGGCTT TGTTGTGAAC CCCATAAAAG CTGTCCCGAC TCCACACTCG 8040 GGGCCGCAGT CCTCTACCCC TGCGTGGTGT ACGACTGTGG GCCCCAGCGC GCTTGGAATA 8100 AAAATCCTCT TGCTGTTTGC ATCAAAAAAA AA 8132 19 base pairs nucleic acid single linear cDNA 4 TGCCTAGAGA CATGTACTC 19 21 base pairs nucleic acid single linear cDNA 5 CCTCTTCTAG CCATTCCTTC A 21 22 base pairs nucleic acid single linear cDNA 6 TCGAGACTCG GTGGAAGGGC CC 22 22 base pairs nucleic acid single linear cDNA 7 GGGCCCTTCC ACCGAGTCTC GA 22 22 base pairs nucleic acid single linear cDNA 8 ACCTGGATCC ATGCATCCCA CG 22 22 base pairs nucleic acid single linear cDNA 9 CGTGGGATGC ATGGATCCAG GT 22 20 base pairs nucleic acid single linear cDNA 10 GGCGCCACCT CCCGATTCGG 20 20 base pairs nucleic acid single linear cDNA 11 CCGAATCGGG AGGTGGCGCC 20 20 base pairs nucleic acid single linear cDNA 12 TCCCCTTAAG CTTCGCCTCC 20 20 base pairs nucleic acid single linear cDNA 13 GGAGGCGAAG CTTAAGGGGA 20 23 base pairs nucleic acid single linear cDNA 14 AAAAGCACAA AGGGCAGGAG AGC 23 23 base pairs nucleic acid single linear cDNA 15 GCTCTCCTGC CCTTTGTGCT TTT 23 20 base pairs nucleic acid single linear cDNA 16 CCTTTAGGAA CCTGGTGGCC 20 20 base pairs nucleic acid single linear cDNA 17 GGCCACCAGG TTCCTAAAGG 20 20 base pairs nucleic acid single linear cDNA 18 CCCCCAGATA TCCTCCATGC 20 20 base pairs nucleic acid single linear cDNA 19 GCATGGAGGA TATCTGGGGG 20 22 base pairs nucleic acid single linear cDNA 20 GCAGTTTCCA ATCAATCCCC AA 22 22 base pairs nucleic acid single linear cDNA 21 TTGGGGATTG ATTGGAAACT GC 22 23 base pairs nucleic acid single linear cDNA 22 TTTATGTTTG CCCAGGACCA CCA 23 23 base pairs nucleic acid single linear cDNA 23 TGGTGGTCCT GGGCAAACAT AAA 23 23 base pairs nucleic acid single linear cDNA 24 GGGAGGTGGC GCCGGCTTAA CGT 23 23 base pairs nucleic acid single linear cDNA 25 ACGTTAAGCC GGCGCCACCT CCC 23 24 base pairs nucleic acid single linear cDNA 26 CCCCCAACCC AAGGACCAGG ACCA 24 24 base pairs nucleic acid single linear cDNA 27 TGGTCCTGGT CCTTGGGTTG GGGG 24 22 base pairs nucleic acid single linear cDNA 28 GCAGCACGAC TAAAATGGGG GC 22 22 base pairs nucleic acid single linear cDNA 29 GCCCCCATTT TAGTCGTGCT GC 22 20 base pairs nucleic acid single linear cDNA 30 CCCCCATCCC ACCAACACCT 20 20 base pairs nucleic acid single linear cDNA 31 AGGTGTTGGT GGGATGGGGG 20 20 base pairs nucleic acid single linear cDNA 32 TCTCCCCCAC CCCGAAACAT 20 20 base pairs nucleic acid single linear cDNA 33 ATGTTTCGGG GTGGGGGAGA 20 24 base pairs nucleic acid single linear cDNA 34 AGCCAAGAAA GCCAGGTCCC CGAA 24 24 base pairs nucleic acid single linear cDNA 35 TTCGGGGACC TGGCTTTCTT GGCT 24 21 base pairs nucleic acid single linear cDNA 36 AGGCTCTGGT GGCGGGTCTC C 21 21 base pairs nucleic acid single linear cDNA 37 GGAGACCCGC CACCAGAGCC T 21 20 base pairs nucleic acid single linear cDNA 38 CCGCAGGGAT GGGTTTGGCA 20 20 base pairs nucleic acid single linear cDNA 39 TGCCAAACCC ATCCCTGCGG 20 22 base pairs nucleic acid single linear cDNA 40 GCTCACCTGG ACCCGACTGC CC 22 22 base pairs nucleic acid single linear cDNA 41 GGGCAGTCGG GTCCAGGTGA GC 22 24 base pairs nucleic acid single linear cDNA 42 GTTTACGGGA CGGGCAGCGA TGGC 24 24 base pairs nucleic acid single linear cDNA 43 GCCATCGCTG CCCGTCCCGT AAAC 24 26 base pairs nucleic acid single linear cDNA 44 TGGCTGGGGC GGCGGTGGTG GACGGG 26 26 base pairs nucleic acid single linear cDNA 45 CCCGTCCACC ACCGCCGCCC CAGCCA 26 24 base pairs nucleic acid single linear cDNA 46 GCCCAAAGCC CCAGAACCCA GACG 24 24 base pairs nucleic acid single linear cDNA 47 CGTCTGGGTT CTGGGGCTTT GGGC 24 20 base pairs nucleic acid single linear cDNA 48 GATGAACAGG CAGACATCTG 20 20 base pairs nucleic acid single linear cDNA 49 CGCTTACAGA CAAGCTGTGA 20 19 base pairs nucleic acid single linear cDNA 50 AGAACAAAGG CTGGGAAGC 19 20 base pairs nucleic acid single linear cDNA 51 ATAGGAGACA GCCTGAACTC 20 20 base pairs nucleic acid single linear cDNA 52 GGACCATTGT CTGACCCTAT 20 20 base pairs nucleic acid single linear cDNA 53 GTCAACACCT ATACCAGCTC 20 20 base pairs nucleic acid single linear cDNA 54 CATCTGAGGT ATAGCAGGTC 20 20 base pairs nucleic acid single linear cDNA 55 GCAGGTGTAG GAACAGGAAC 20 20 base pairs nucleic acid single linear cDNA 56 ACCTGTTGAA CCATCCCTCA 20 20 base pairs nucleic acid single linear cDNA 57 CGAATGGAGA GATCCAGGTA 20 20 base pairs nucleic acid single linear cDNA 58 CCTGCATCAC TTCTCTTACC 20 20 base pairs nucleic acid single linear cDNA 59 TTGCCTGCTT GTGGAATACG 20 21 base pairs nucleic acid single linear cDNA 60 CAAGAGAAGA AGTGGGGAAT G 21 20 base pairs nucleic acid single linear cDNA 61 CACAGTCGTA CACCACGCAG 20 20 base pairs nucleic acid single linear cDNA 62 GGGAGACAGA AGAAGAAAGG 20 20 base pairs nucleic acid single linear cDNA 63 CGATAGTCAT TAGTCCCAGG 20 21 base pairs nucleic acid single linear cDNA 64 TGCTGGTTTG CATCAAGACC G 21 20 base pairs nucleic acid single linear cDNA 65 GTCGCAAAGG CATACCTGCT 20 20 base pairs nucleic acid single linear cDNA 66 ACAGAGCCTC TGCTAAGAAG 20 19 base pairs nucleic acid single linear cDNA 67 GCAGCTGTTG ACAATCATC 19 20 base pairs nucleic acid single linear cDNA 68 TATGAGGAGA GGGCTTGACT 20 19 base pairs nucleic acid single linear cDNA 69 AGCAGACGTG CTAGGAGGT 19 19 base pairs nucleic acid single linear cDNA 70 TCCTCTTGCT GTTTGCATC 19 20 base pairs nucleic acid single linear cDNA 71 CAGACACTCA GAACAGAGAC 20 20 base pairs nucleic acid single linear cDNA 72 ACATCGTCTA ACCCACCTAG 20 21 base pairs nucleic acid single linear cDNA 73 CTCGTTTCTG GTCATACCTG A 21 19 base pairs nucleic acid single linear cDNA 74 GAGTACATCT CTCTAGGCA 19 

What is claimed is:
 1. A polypeptide encoded by a nucleic acid molecule at least 85% identical to a molecule selected from the group consisting of: (a) SEQ ID NO:1; (b) the fully complementary sequence of SEQ ID NO:1; (c) SEQ ID NO:2; (d) the fully complementary sequence of SEQ ID NO:2; (e) SEQ ID NO:3; and (f) the fully complementary sequence of SEQ ID NO:3.
 2. The polypeptide of claim 1 that is encoded by SEQ ID NO:1.
 3. The polypeptide of claim 1 that is encoded by the fully complementary sequence of SEQ ID NO:1.
 4. The polypeptide of claim 1 that is encoded by SEQ ID NO:2.
 5. The polypeptide of claim 1 that is encoded by the fully complementary sequence of SEQ ID NO:2.
 6. The polypeptide of claim 1 that is encoded by SEQ ID NO:3.
 7. The polypeptide of claim 1 that is encoded by the fully complementary sequence of SEQ ID NO:3.
 8. A polypeptide encoded by a nucleic acid molecule selected from the group consisting of: (a) nucleotides 2-1999 of SEQ ID NO:1 (env); (b) nucleotides 2452-4839 of SEQ ID NO:1 (gag); (c) nucleotides 4871-8060 of SEQ ID NO:11 (pol); (d) nucleotides 598-2169 of SEQ ID NO:2 (gag); (e) nucleotides 2320-4737 of SEQ ID NO:2 (pol); (f) nucleotides 4738-6722 of SEQ BD NO:2 (env); (g) nucleotides 585-2156 of SEQ ID NO:3 (gag); (h) nucleotides 2307-5741 of SEQ ID NO:3 (pol); and (i) nucleotides 5620-7533 of SEQ ID NO:3 (env).
 9. The polypeptide of claim 8 that is encoded by nucleotides 2-1999 of SEQ ID NO:1.
 10. The polypeptide of claim 8 that is encoded by nucleotides 2452-4839 of SEQ ID NO:1.
 11. The polypeptide of claim 8 that is encoded by nucleotides 4871-8060 of SEQ ID NO:1.
 12. The polypeptide of claim 8 that is encoded by nucleotides 598-2169 of SEQ ID NO:2.
 13. The polypeptide of claim 8 that is encoded by nucleotides 2320-4737 of SEQ ID NO:2.
 14. The polypeptide of claim 8 that is encoded by nucleotides 4738-6722 of SEQ ID NO:2.
 15. The polypeptide of claim 8 that is encoded by nucleotides 585-2156 of SEQ ID NO:3.
 16. The polypeptide of claim 8 that is encoded by nucleotides 2307-5741 of SEQ ID NO:3.
 17. The polypeptide of claim 8 that is encoded by nucleotides 5620-7533 of SEQ ID NO:3.
 18. A polypeptide encoded by a sequence at least 15 base pairs in length selected from a polynucleotide sequence, the polynucleotide sequence selected from the group consisting of: (a) SEQ ID NO:1; (b) the fully complementary sequence of SEQ ID NO:1; (c) SEQ ID NO:2; (d) the fully complementary sequence of SEQ ID NO:2; (e) SEQ ID NO:3; (f) the fully complementary sequence of SEQ ID NO:3; and further characterized by having less than 70% homology with the corresponding region in human, mouse and primate retroviral sequences, wherein the last five 3′ bases are unique to the selected sequence.
 19. The polypeptide of claim 18, wherein the sequence of at least 15 base pairs is selected from SEQ ID NO:1.
 20. The polypeptide of claim 18, wherein the sequence of at least 15 base pairs is selected from the fully complementary sequence of SEQ ID NO:1.
 21. The polypeptide of claim 18, wherein the sequence of at least 15 base pairs is selected from SEQ ID NO:2.
 22. The polypeptide of claim 18, wherein the sequence of at least 15 base pairs is selected from the fully complementary sequence of SEQ ID NO:2.
 23. The polypeptide of claim 18, wherein the sequence of at least 15 base pairs is selected from SEQ ID NO:3.
 24. The polypeptide of claim 18, wherein the sequence of at least 15 base pairs is selected from the fully complementary sequence of SEQ ID NO:3.
 25. A polypeptide encoded by a sequence selected from the group consisting of SEQ ID NO:4 through SEQ ID NO:74.
 26. A polypeptide encoded by a sequence at least 20 nucleotides in length that hybridizes under stringent conditions to a molecule selected from the group consisting of (a) SED ID NO:1; (b) the fully complementary sequence of SEQ ID NO:1; (c) SEQ ID NO:2; (d) the fully complementary sequence of SEQ ID NO:2; (e) SEQ ID NO:3; and (f) the fully complementary sequence of SEQ ID NO:3. 